diff --git a/packages/core/src/hooks/hookPlanner.test.ts b/packages/core/src/hooks/hookPlanner.test.ts
new file mode 100644
index 0000000000..c408266ecb
--- /dev/null
+++ b/packages/core/src/hooks/hookPlanner.test.ts
@@ -0,0 +1,324 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import { HookPlanner } from './hookPlanner.js';
+import type { HookRegistry, HookRegistryEntry } from './hookRegistry.js';
+import { HookEventName, HookType } from './types.js';
+import { ConfigSource } from './hookRegistry.js';
+
+// Mock debugLogger using vi.hoisted
+const mockDebugLogger = vi.hoisted(() => ({
+  log: vi.fn(),
+  warn: vi.fn(),
+  error: vi.fn(),
+  debug: vi.fn(),
+}));
+
+vi.mock('../utils/debugLogger.js', () => ({
+  debugLogger: mockDebugLogger,
+}));
+
+describe('HookPlanner', () => {
+  let hookPlanner: HookPlanner;
+  let mockHookRegistry: HookRegistry;
+
+  beforeEach(() => {
+    vi.resetAllMocks();
+
+    mockHookRegistry = {
+      getHooksForEvent: vi.fn(),
+    } as unknown as HookRegistry;
+
+    hookPlanner = new HookPlanner(mockHookRegistry);
+  });
+
+  describe('createExecutionPlan', () => {
+    it('should return empty plan when no hooks registered', () => {
+      vi.mocked(mockHookRegistry.getHooksForEvent).mockReturnValue([]);
+
+      const plan = hookPlanner.createExecutionPlan(HookEventName.BeforeTool);
+
+      expect(plan).toBeNull();
+    });
+
+    it('should create plan for hooks without matchers', () => {
+      const mockEntries: HookRegistryEntry[] = [
+        {
+          config: { type: HookType.Command, command: './hook1.sh' },
+          source: ConfigSource.Project,
+          eventName: HookEventName.BeforeTool,
+          enabled: true,
+        },
+        {
+          config: {
+            type: HookType.Command,
+            command: './test-hook.sh',
+          },
+          source: ConfigSource.User,
+          eventName: HookEventName.BeforeTool,
+          enabled: true,
+        },
+      ];
+
+      vi.mocked(mockHookRegistry.getHooksForEvent).mockReturnValue(mockEntries);
+
+      const plan = hookPlanner.createExecutionPlan(HookEventName.BeforeTool);
+
+      expect(plan).not.toBeNull();
+      expect(plan!.hookConfigs).toHaveLength(2);
+      expect(plan!.hookConfigs[0].command).toBe('./hook1.sh');
+      expect(plan!.hookConfigs[1].command).toBe('./test-hook.sh');
+    });
+
+    it('should filter hooks by tool name matcher', () => {
+      const mockEntries: HookRegistryEntry[] = [
+        {
+          config: { type: HookType.Command, command: './edit_hook.sh' },
+          source: ConfigSource.Project,
+          eventName: HookEventName.BeforeTool,
+          matcher: 'EditTool',
+          enabled: true,
+        },
+        {
+          config: { type: HookType.Command, command: './general_hook.sh' },
+          source: ConfigSource.Project,
+          eventName: HookEventName.BeforeTool,
+          enabled: true,
+        },
+      ];
+
+      vi.mocked(mockHookRegistry.getHooksForEvent).mockReturnValue(mockEntries);
+
+      // Test with EditTool context
+      const plan = hookPlanner.createExecutionPlan(HookEventName.BeforeTool, {
+        toolName: 'EditTool',
+      });
+
+      expect(plan).not.toBeNull();
+      expect(plan!.hookConfigs).toHaveLength(2); // Both should match (one specific, one general)
+    });
+
+    it('should filter hooks by regex matcher', () => {
+      const mockEntries: HookRegistryEntry[] = [
+        {
+          config: { type: HookType.Command, command: './edit_hook.sh' },
+          source: ConfigSource.Project,
+          eventName: HookEventName.BeforeTool,
+          matcher: 'Edit|Write',
+          enabled: true,
+        },
+        {
+          config: { type: HookType.Command, command: './read_hook.sh' },
+          source: ConfigSource.Project,
+          eventName: HookEventName.BeforeTool,
+          matcher: 'ReadTool',
+          enabled: true,
+        },
+      ];
+
+      vi.mocked(mockHookRegistry.getHooksForEvent).mockReturnValue(mockEntries);
+
+      // Test with EditTool - should match first hook
+      const editPlan = hookPlanner.createExecutionPlan(
+        HookEventName.BeforeTool,
+        { toolName: 'EditTool' },
+      );
+      expect(editPlan).not.toBeNull();
+      expect(editPlan!.hookConfigs).toHaveLength(1);
+      expect(editPlan!.hookConfigs[0].command).toBe('./edit_hook.sh');
+
+      // Test with WriteTool - should match first hook
+      const writePlan = hookPlanner.createExecutionPlan(
+        HookEventName.BeforeTool,
+        { toolName: 'WriteTool' },
+      );
+      expect(writePlan).not.toBeNull();
+      expect(writePlan!.hookConfigs).toHaveLength(1);
+      expect(writePlan!.hookConfigs[0].command).toBe('./edit_hook.sh');
+
+      // Test with ReadTool - should match second hook
+      const readPlan = hookPlanner.createExecutionPlan(
+        HookEventName.BeforeTool,
+        { toolName: 'ReadTool' },
+      );
+      expect(readPlan).not.toBeNull();
+      expect(readPlan!.hookConfigs).toHaveLength(1);
+      expect(readPlan!.hookConfigs[0].command).toBe('./read_hook.sh');
+
+      // Test with unmatched tool - should match no hooks
+      const otherPlan = hookPlanner.createExecutionPlan(
+        HookEventName.BeforeTool,
+        { toolName: 'OtherTool' },
+      );
+      expect(otherPlan).toBeNull();
+    });
+
+    it('should handle wildcard matcher', () => {
+      const mockEntries: HookRegistryEntry[] = [
+        {
+          config: { type: HookType.Command, command: './wildcard_hook.sh' },
+          source: ConfigSource.Project,
+          eventName: HookEventName.BeforeTool,
+          matcher: '*',
+          enabled: true,
+        },
+      ];
+
+      vi.mocked(mockHookRegistry.getHooksForEvent).mockReturnValue(mockEntries);
+
+      const plan = hookPlanner.createExecutionPlan(HookEventName.BeforeTool, {
+        toolName: 'AnyTool',
+      });
+
+      expect(plan).not.toBeNull();
+      expect(plan!.hookConfigs).toHaveLength(1);
+    });
+
+    it('should handle empty string matcher', () => {
+      const mockEntries: HookRegistryEntry[] = [
+        {
+          config: {
+            type: HookType.Command,
+            command: './empty_matcher_hook.sh',
+          },
+          source: ConfigSource.Project,
+          eventName: HookEventName.BeforeTool,
+          matcher: '',
+          enabled: true,
+        },
+      ];
+
+      vi.mocked(mockHookRegistry.getHooksForEvent).mockReturnValue(mockEntries);
+
+      const plan = hookPlanner.createExecutionPlan(HookEventName.BeforeTool, {
+        toolName: 'AnyTool',
+      });
+
+      expect(plan).not.toBeNull();
+      expect(plan!.hookConfigs).toHaveLength(1);
+    });
+
+    it('should handle invalid regex matcher gracefully', () => {
+      const mockEntries: HookRegistryEntry[] = [
+        {
+          config: {
+            type: HookType.Command,
+            command: './invalid_regex_hook.sh',
+          },
+          source: ConfigSource.Project,
+          eventName: HookEventName.BeforeTool,
+          matcher: '[invalid-regex',
+          enabled: true,
+        },
+      ];
+
+      vi.mocked(mockHookRegistry.getHooksForEvent).mockReturnValue(mockEntries);
+
+      // Should match when toolName exactly equals the invalid regex pattern
+      const plan = hookPlanner.createExecutionPlan(HookEventName.BeforeTool, {
+        toolName: '[invalid-regex',
+      });
+
+      expect(plan).not.toBeNull();
+      expect(plan!.hookConfigs).toHaveLength(1); // Should fall back to exact match
+
+      // Should not match when toolName doesn't exactly equal the pattern
+      const planNoMatch = hookPlanner.createExecutionPlan(
+        HookEventName.BeforeTool,
+        {
+          toolName: 'other-tool',
+        },
+      );
+
+      expect(planNoMatch).toBeNull();
+    });
+
+    it('should deduplicate identical hooks', () => {
+      const mockEntries: HookRegistryEntry[] = [
+        {
+          config: { type: HookType.Command, command: './same_hook.sh' },
+          source: ConfigSource.Project,
+          eventName: HookEventName.BeforeTool,
+          enabled: true,
+        },
+        {
+          config: { type: HookType.Command, command: './same_hook.sh' },
+          source: ConfigSource.User,
+          eventName: HookEventName.BeforeTool,
+          enabled: true,
+        },
+        {
+          config: {
+            type: HookType.Command,
+            command: './test-hook.sh',
+          },
+          source: ConfigSource.Project,
+          eventName: HookEventName.BeforeTool,
+          enabled: true,
+        },
+        {
+          config: {
+            type: HookType.Command,
+            command: './test-hook.sh',
+          },
+          source: ConfigSource.User,
+          eventName: HookEventName.BeforeTool,
+          enabled: true,
+        },
+      ];
+
+      vi.mocked(mockHookRegistry.getHooksForEvent).mockReturnValue(mockEntries);
+
+      const plan = hookPlanner.createExecutionPlan(HookEventName.BeforeTool);
+
+      expect(plan).not.toBeNull();
+      expect(plan!.hookConfigs).toHaveLength(2); // Should be deduplicated to 2 unique hooks
+      expect(mockDebugLogger.debug).toHaveBeenCalledWith(
+        expect.stringContaining('Deduplicated hook'),
+      );
+    });
+
+    it('should match trigger for session events', () => {
+      const mockEntries: HookRegistryEntry[] = [
+        {
+          config: { type: HookType.Command, command: './startup_hook.sh' },
+          source: ConfigSource.Project,
+          eventName: HookEventName.SessionStart,
+          matcher: 'startup',
+          enabled: true,
+        },
+        {
+          config: { type: HookType.Command, command: './resume_hook.sh' },
+          source: ConfigSource.Project,
+          eventName: HookEventName.SessionStart,
+          matcher: 'resume',
+          enabled: true,
+        },
+      ];
+
+      vi.mocked(mockHookRegistry.getHooksForEvent).mockReturnValue(mockEntries);
+
+      // Test startup trigger
+      const startupPlan = hookPlanner.createExecutionPlan(
+        HookEventName.SessionStart,
+        { trigger: 'startup' },
+      );
+      expect(startupPlan).not.toBeNull();
+      expect(startupPlan!.hookConfigs).toHaveLength(1);
+      expect(startupPlan!.hookConfigs[0].command).toBe('./startup_hook.sh');
+
+      // Test resume trigger
+      const resumePlan = hookPlanner.createExecutionPlan(
+        HookEventName.SessionStart,
+        { trigger: 'resume' },
+      );
+      expect(resumePlan).not.toBeNull();
+      expect(resumePlan!.hookConfigs).toHaveLength(1);
+      expect(resumePlan!.hookConfigs[0].command).toBe('./resume_hook.sh');
+    });
+  });
+});
diff --git a/packages/core/src/hooks/hookPlanner.ts b/packages/core/src/hooks/hookPlanner.ts
new file mode 100644
index 0000000000..4a0f00a8e1
--- /dev/null
+++ b/packages/core/src/hooks/hookPlanner.ts
@@ -0,0 +1,154 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import type { HookRegistry, HookRegistryEntry } from './hookRegistry.js';
+import type { HookExecutionPlan } from './types.js';
+import type { HookEventName } from './types.js';
+import { debugLogger } from '../utils/debugLogger.js';
+
+/**
+ * Hook planner that selects matching hooks and creates execution plans
+ */
+export class HookPlanner {
+  private readonly hookRegistry: HookRegistry;
+
+  constructor(hookRegistry: HookRegistry) {
+    this.hookRegistry = hookRegistry;
+  }
+
+  /**
+   * Create execution plan for a hook event
+   */
+  createExecutionPlan(
+    eventName: HookEventName,
+    context?: HookEventContext,
+  ): HookExecutionPlan | null {
+    const hookEntries = this.hookRegistry.getHooksForEvent(eventName);
+
+    if (hookEntries.length === 0) {
+      return null;
+    }
+
+    // Filter hooks by matcher
+    const matchingEntries = hookEntries.filter((entry) =>
+      this.matchesContext(entry, context),
+    );
+
+    if (matchingEntries.length === 0) {
+      return null;
+    }
+
+    // Deduplicate identical hooks
+    const deduplicatedEntries = this.deduplicateHooks(matchingEntries);
+
+    // Extract hook configs
+    const hookConfigs = deduplicatedEntries.map((entry) => entry.config);
+
+    // Determine execution strategy - if ANY hook definition has sequential=true, run all sequentially
+    const sequential = deduplicatedEntries.some(
+      (entry) => entry.sequential === true,
+    );
+
+    const plan: HookExecutionPlan = {
+      eventName,
+      hookConfigs,
+      sequential,
+    };
+
+    debugLogger.debug(
+      `Created execution plan for ${eventName}: ${hookConfigs.length} hook(s) to execute ${sequential ? 'sequentially' : 'in parallel'}`,
+    );
+
+    return plan;
+  }
+
+  /**
+   * Check if a hook entry matches the given context
+   */
+  private matchesContext(
+    entry: HookRegistryEntry,
+    context?: HookEventContext,
+  ): boolean {
+    if (!entry.matcher || !context) {
+      return true; // No matcher means match all
+    }
+
+    const matcher = entry.matcher.trim();
+
+    if (matcher === '' || matcher === '*') {
+      return true; // Empty string or wildcard matches all
+    }
+
+    // For tool events, match against tool name
+    if (context.toolName) {
+      return this.matchesToolName(matcher, context.toolName);
+    }
+
+    // For other events, match against trigger/source
+    if (context.trigger) {
+      return this.matchesTrigger(matcher, context.trigger);
+    }
+
+    return true;
+  }
+
+  /**
+   * Match tool name against matcher pattern
+   */
+  private matchesToolName(matcher: string, toolName: string): boolean {
+    try {
+      // Attempt to treat the matcher as a regular expression.
+      const regex = new RegExp(matcher);
+      return regex.test(toolName);
+    } catch {
+      // If it's not a valid regex, treat it as a literal string for an exact match.
+      return matcher === toolName;
+    }
+  }
+
+  /**
+   * Match trigger/source against matcher pattern
+   */
+  private matchesTrigger(matcher: string, trigger: string): boolean {
+    return matcher === trigger;
+  }
+
+  /**
+   * Deduplicate identical hook configurations
+   */
+  private deduplicateHooks(entries: HookRegistryEntry[]): HookRegistryEntry[] {
+    const seen = new Set<string>();
+    const deduplicated: HookRegistryEntry[] = [];
+
+    for (const entry of entries) {
+      const key = this.getHookKey(entry);
+
+      if (!seen.has(key)) {
+        seen.add(key);
+        deduplicated.push(entry);
+      } else {
+        debugLogger.debug(`Deduplicated hook: ${key}`);
+      }
+    }
+
+    return deduplicated;
+  }
+
+  /**
+   * Generate a unique key for a hook entry
+   */
+  private getHookKey(entry: HookRegistryEntry): string {
+    return `command:${entry.config.command}`;
+  }
+}
+
+/**
+ * Context information for hook event matching
+ */
+export interface HookEventContext {
+  toolName?: string;
+  trigger?: string;
+}
diff --git a/packages/core/src/hooks/hookRegistry.test.ts b/packages/core/src/hooks/hookRegistry.test.ts
new file mode 100644
index 0000000000..5c6906b838
--- /dev/null
+++ b/packages/core/src/hooks/hookRegistry.test.ts
@@ -0,0 +1,504 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
+import * as fs from 'node:fs';
+import {
+  HookRegistry,
+  ConfigSource,
+  HookRegistryNotInitializedError,
+} from './hookRegistry.js';
+import type { Storage } from '../config/storage.js';
+import { HookEventName, HookType } from './types.js';
+import type { Config } from '../config/config.js';
+import type { HookDefinition } from './types.js';
+
+// Mock fs
+vi.mock('fs', () => ({
+  existsSync: vi.fn(),
+  readFileSync: vi.fn(),
+}));
+
+// Mock debugLogger using vi.hoisted
+const mockDebugLogger = vi.hoisted(() => ({
+  log: vi.fn(),
+  warn: vi.fn(),
+  error: vi.fn(),
+  debug: vi.fn(),
+}));
+
+vi.mock('../utils/debugLogger.js', () => ({
+  debugLogger: mockDebugLogger,
+}));
+
+describe('HookRegistry', () => {
+  let hookRegistry: HookRegistry;
+  let mockConfig: Config;
+  let mockStorage: Storage;
+
+  beforeEach(() => {
+    vi.resetAllMocks();
+
+    mockStorage = {
+      getGeminiDir: vi.fn().mockReturnValue('/project/.gemini'),
+    } as unknown as Storage;
+
+    mockConfig = {
+      storage: mockStorage,
+      getExtensions: vi.fn().mockReturnValue([]),
+      getHooks: vi.fn().mockReturnValue({}),
+    } as unknown as Config;
+
+    hookRegistry = new HookRegistry(mockConfig);
+  });
+
+  afterEach(() => {
+    vi.restoreAllMocks();
+  });
+
+  describe('initialize', () => {
+    it('should initialize successfully with no hooks', async () => {
+      vi.mocked(fs.existsSync).mockReturnValue(false);
+
+      await hookRegistry.initialize();
+
+      expect(hookRegistry.getAllHooks()).toHaveLength(0);
+      expect(mockDebugLogger.log).toHaveBeenCalledWith(
+        'Hook registry initialized with 0 hook entries',
+      );
+    });
+
+    it('should load hooks from project configuration', async () => {
+      const mockHooksConfig = {
+        BeforeTool: [
+          {
+            matcher: 'EditTool',
+            hooks: [
+              {
+                type: 'command',
+                command: './hooks/check_style.sh',
+                timeout: 60,
+              },
+            ],
+          },
+        ],
+      };
+
+      // Update mock to return the hooks configuration
+      vi.mocked(mockConfig.getHooks).mockReturnValue(
+        mockHooksConfig as unknown as {
+          [K in HookEventName]?: HookDefinition[];
+        },
+      );
+
+      await hookRegistry.initialize();
+
+      const hooks = hookRegistry.getAllHooks();
+      expect(hooks).toHaveLength(1);
+      expect(hooks[0].eventName).toBe(HookEventName.BeforeTool);
+      expect(hooks[0].config.type).toBe(HookType.Command);
+      expect(hooks[0].config.command).toBe('./hooks/check_style.sh');
+      expect(hooks[0].matcher).toBe('EditTool');
+      expect(hooks[0].source).toBe(ConfigSource.Project);
+    });
+
+    it('should load plugin hooks', async () => {
+      const mockHooksConfig = {
+        AfterTool: [
+          {
+            hooks: [
+              {
+                type: 'command',
+                command: './hooks/after-tool.sh',
+                timeout: 30,
+              },
+            ],
+          },
+        ],
+      };
+
+      // Update mock to return the hooks configuration
+      vi.mocked(mockConfig.getHooks).mockReturnValue(
+        mockHooksConfig as unknown as {
+          [K in HookEventName]?: HookDefinition[];
+        },
+      );
+
+      await hookRegistry.initialize();
+
+      const hooks = hookRegistry.getAllHooks();
+      expect(hooks).toHaveLength(1);
+      expect(hooks[0].eventName).toBe(HookEventName.AfterTool);
+      expect(hooks[0].config.type).toBe(HookType.Command);
+      expect(hooks[0].config.command).toBe('./hooks/after-tool.sh');
+    });
+
+    it('should handle invalid configuration gracefully', async () => {
+      const invalidHooksConfig = {
+        BeforeTool: [
+          {
+            hooks: [
+              {
+                type: 'invalid-type', // Invalid hook type
+                command: './hooks/test.sh',
+              },
+            ],
+          },
+        ],
+      };
+
+      // Update mock to return invalid configuration
+      vi.mocked(mockConfig.getHooks).mockReturnValue(
+        invalidHooksConfig as unknown as {
+          [K in HookEventName]?: HookDefinition[];
+        },
+      );
+
+      await hookRegistry.initialize();
+
+      expect(hookRegistry.getAllHooks()).toHaveLength(0);
+      expect(mockDebugLogger.warn).toHaveBeenCalled();
+    });
+
+    it('should validate hook configurations', async () => {
+      const mockHooksConfig = {
+        BeforeTool: [
+          {
+            hooks: [
+              {
+                type: 'invalid',
+                command: './hooks/test.sh',
+              },
+              {
+                type: 'command',
+                // Missing command field
+              },
+            ],
+          },
+        ],
+      };
+
+      // Update mock to return invalid configuration
+      vi.mocked(mockConfig.getHooks).mockReturnValue(
+        mockHooksConfig as unknown as {
+          [K in HookEventName]?: HookDefinition[];
+        },
+      );
+
+      await hookRegistry.initialize();
+
+      expect(hookRegistry.getAllHooks()).toHaveLength(0);
+      expect(mockDebugLogger.warn).toHaveBeenCalled(); // At least some warnings should be logged
+    });
+  });
+
+  describe('getHooksForEvent', () => {
+    beforeEach(async () => {
+      const mockHooksConfig = {
+        BeforeTool: [
+          {
+            matcher: 'EditTool',
+            hooks: [
+              {
+                type: 'command',
+                command: './hooks/edit_check.sh',
+              },
+            ],
+          },
+          {
+            hooks: [
+              {
+                type: 'command',
+                command: './hooks/general_check.sh',
+              },
+            ],
+          },
+        ],
+        AfterTool: [
+          {
+            hooks: [
+              {
+                type: 'command',
+                command: './hooks/after-tool.sh',
+              },
+            ],
+          },
+        ],
+      };
+
+      // Update mock to return the hooks configuration
+      vi.mocked(mockConfig.getHooks).mockReturnValue(
+        mockHooksConfig as unknown as {
+          [K in HookEventName]?: HookDefinition[];
+        },
+      );
+
+      await hookRegistry.initialize();
+    });
+
+    it('should return hooks for specific event', () => {
+      const beforeToolHooks = hookRegistry.getHooksForEvent(
+        HookEventName.BeforeTool,
+      );
+      expect(beforeToolHooks).toHaveLength(2);
+
+      const afterToolHooks = hookRegistry.getHooksForEvent(
+        HookEventName.AfterTool,
+      );
+      expect(afterToolHooks).toHaveLength(1);
+    });
+
+    it('should return empty array for events with no hooks', () => {
+      const notificationHooks = hookRegistry.getHooksForEvent(
+        HookEventName.Notification,
+      );
+      expect(notificationHooks).toHaveLength(0);
+    });
+
+    it('should throw error if not initialized', () => {
+      const uninitializedRegistry = new HookRegistry(mockConfig);
+
+      expect(() => {
+        uninitializedRegistry.getHooksForEvent(HookEventName.BeforeTool);
+      }).toThrow(HookRegistryNotInitializedError);
+    });
+  });
+
+  describe('setHookEnabled', () => {
+    beforeEach(async () => {
+      const mockHooksConfig = {
+        BeforeTool: [
+          {
+            hooks: [
+              {
+                type: 'command',
+                command: './hooks/test.sh',
+              },
+            ],
+          },
+        ],
+      };
+
+      // Update mock to return the hooks configuration
+      vi.mocked(mockConfig.getHooks).mockReturnValue(
+        mockHooksConfig as unknown as {
+          [K in HookEventName]?: HookDefinition[];
+        },
+      );
+
+      await hookRegistry.initialize();
+    });
+
+    it('should enable and disable hooks', () => {
+      const hookName = './hooks/test.sh';
+
+      // Initially enabled
+      let hooks = hookRegistry.getHooksForEvent(HookEventName.BeforeTool);
+      expect(hooks).toHaveLength(1);
+
+      // Disable
+      hookRegistry.setHookEnabled(hookName, false);
+      hooks = hookRegistry.getHooksForEvent(HookEventName.BeforeTool);
+      expect(hooks).toHaveLength(0);
+
+      // Re-enable
+      hookRegistry.setHookEnabled(hookName, true);
+      hooks = hookRegistry.getHooksForEvent(HookEventName.BeforeTool);
+      expect(hooks).toHaveLength(1);
+    });
+
+    it('should warn when hook not found', () => {
+      hookRegistry.setHookEnabled('non-existent-hook', false);
+      expect(mockDebugLogger.warn).toHaveBeenCalledWith(
+        'No hooks found matching "non-existent-hook"',
+      );
+    });
+  });
+
+  describe('malformed configuration handling', () => {
+    it('should handle non-array definitions gracefully', async () => {
+      const malformedConfig = {
+        BeforeTool: 'not-an-array', // Should be an array of HookDefinition
+      };
+
+      vi.mocked(mockConfig.getHooks).mockReturnValue(
+        malformedConfig as unknown as {
+          [K in HookEventName]?: HookDefinition[];
+        },
+      );
+
+      await hookRegistry.initialize();
+
+      expect(hookRegistry.getAllHooks()).toHaveLength(0);
+      expect(mockDebugLogger.warn).toHaveBeenCalledWith(
+        expect.stringContaining('is not an array'),
+      );
+    });
+
+    it('should handle object instead of array for definitions', async () => {
+      const malformedConfig = {
+        AfterTool: { hooks: [] }, // Should be an array, not a single object
+      };
+
+      vi.mocked(mockConfig.getHooks).mockReturnValue(
+        malformedConfig as unknown as {
+          [K in HookEventName]?: HookDefinition[];
+        },
+      );
+
+      await hookRegistry.initialize();
+
+      expect(hookRegistry.getAllHooks()).toHaveLength(0);
+      expect(mockDebugLogger.warn).toHaveBeenCalledWith(
+        expect.stringContaining('is not an array'),
+      );
+    });
+
+    it('should handle null definition gracefully', async () => {
+      const malformedConfig = {
+        BeforeTool: [null], // Invalid: null definition
+      };
+
+      vi.mocked(mockConfig.getHooks).mockReturnValue(
+        malformedConfig as unknown as {
+          [K in HookEventName]?: HookDefinition[];
+        },
+      );
+
+      await hookRegistry.initialize();
+
+      expect(hookRegistry.getAllHooks()).toHaveLength(0);
+      expect(mockDebugLogger.warn).toHaveBeenCalledWith(
+        expect.stringContaining('Discarding invalid hook definition'),
+        null,
+      );
+    });
+
+    it('should handle definition without hooks array', async () => {
+      const malformedConfig = {
+        BeforeTool: [
+          {
+            matcher: 'EditTool',
+            // Missing hooks array
+          },
+        ],
+      };
+
+      vi.mocked(mockConfig.getHooks).mockReturnValue(
+        malformedConfig as unknown as {
+          [K in HookEventName]?: HookDefinition[];
+        },
+      );
+
+      await hookRegistry.initialize();
+
+      expect(hookRegistry.getAllHooks()).toHaveLength(0);
+      expect(mockDebugLogger.warn).toHaveBeenCalledWith(
+        expect.stringContaining('Discarding invalid hook definition'),
+        expect.objectContaining({ matcher: 'EditTool' }),
+      );
+    });
+
+    it('should handle non-array hooks property', async () => {
+      const malformedConfig = {
+        BeforeTool: [
+          {
+            matcher: 'EditTool',
+            hooks: 'not-an-array', // Should be an array
+          },
+        ],
+      };
+
+      vi.mocked(mockConfig.getHooks).mockReturnValue(
+        malformedConfig as unknown as {
+          [K in HookEventName]?: HookDefinition[];
+        },
+      );
+
+      await hookRegistry.initialize();
+
+      expect(hookRegistry.getAllHooks()).toHaveLength(0);
+      expect(mockDebugLogger.warn).toHaveBeenCalledWith(
+        expect.stringContaining('Discarding invalid hook definition'),
+        expect.objectContaining({ hooks: 'not-an-array', matcher: 'EditTool' }),
+      );
+    });
+
+    it('should handle non-object hookConfig in hooks array', async () => {
+      const malformedConfig = {
+        BeforeTool: [
+          {
+            hooks: [
+              'not-an-object', // Should be an object
+              42, // Should be an object
+              null, // Should be an object
+            ],
+          },
+        ],
+      };
+
+      vi.mocked(mockConfig.getHooks).mockReturnValue(
+        malformedConfig as unknown as {
+          [K in HookEventName]?: HookDefinition[];
+        },
+      );
+
+      await hookRegistry.initialize();
+
+      expect(hookRegistry.getAllHooks()).toHaveLength(0);
+      expect(mockDebugLogger.warn).toHaveBeenCalledTimes(3); // One warning for each invalid hookConfig
+    });
+
+    it('should handle mixed valid and invalid hook configurations', async () => {
+      const mixedConfig = {
+        BeforeTool: [
+          {
+            hooks: [
+              {
+                type: 'command',
+                command: './valid-hook.sh',
+              },
+              'invalid-string',
+              {
+                type: 'invalid-type',
+                command: './invalid-type.sh',
+              },
+            ],
+          },
+        ],
+      };
+
+      vi.mocked(mockConfig.getHooks).mockReturnValue(
+        mixedConfig as unknown as {
+          [K in HookEventName]?: HookDefinition[];
+        },
+      );
+
+      await hookRegistry.initialize();
+
+      // Should only load the valid hook
+      const hooks = hookRegistry.getAllHooks();
+      expect(hooks).toHaveLength(1);
+      expect(hooks[0].config.command).toBe('./valid-hook.sh');
+
+      // Verify the warnings for invalid configurations
+      // 1st warning: non-object hookConfig ('invalid-string')
+      expect(mockDebugLogger.warn).toHaveBeenCalledWith(
+        expect.stringContaining('Discarding invalid hook configuration'),
+        'invalid-string',
+      );
+      // 2nd warning: validateHookConfig logs invalid type
+      expect(mockDebugLogger.warn).toHaveBeenCalledWith(
+        expect.stringContaining('Invalid hook BeforeTool from project type'),
+      );
+      // 3rd warning: processHookDefinition logs the failed hookConfig
+      expect(mockDebugLogger.warn).toHaveBeenCalledWith(
+        expect.stringContaining('Discarding invalid hook configuration'),
+        expect.objectContaining({ type: 'invalid-type' }),
+      );
+    });
+  });
+});
diff --git a/packages/core/src/hooks/hookRegistry.ts b/packages/core/src/hooks/hookRegistry.ts
new file mode 100644
index 0000000000..82fda32975
--- /dev/null
+++ b/packages/core/src/hooks/hookRegistry.ts
@@ -0,0 +1,273 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import type { Config } from '../config/config.js';
+import type { HookDefinition, HookConfig } from './types.js';
+import { HookEventName } from './types.js';
+import { debugLogger } from '../utils/debugLogger.js';
+
+/**
+ * Error thrown when attempting to use HookRegistry before initialization
+ */
+export class HookRegistryNotInitializedError extends Error {
+  constructor(message = 'Hook registry not initialized') {
+    super(message);
+    this.name = 'HookRegistryNotInitializedError';
+  }
+}
+
+/**
+ * Configuration source levels in precedence order (highest to lowest)
+ */
+export enum ConfigSource {
+  Project = 'project',
+  User = 'user',
+  System = 'system',
+  Extensions = 'extensions',
+}
+
+/**
+ * Hook registry entry with source information
+ */
+export interface HookRegistryEntry {
+  config: HookConfig;
+  source: ConfigSource;
+  eventName: HookEventName;
+  matcher?: string;
+  sequential?: boolean;
+  enabled: boolean;
+}
+
+/**
+ * Hook registry that loads and validates hook definitions from multiple sources
+ */
+export class HookRegistry {
+  private readonly config: Config;
+  private entries: HookRegistryEntry[] = [];
+  private initialized = false;
+
+  constructor(config: Config) {
+    this.config = config;
+  }
+
+  /**
+   * Initialize the registry by processing hooks from config
+   */
+  async initialize(): Promise<void> {
+    if (this.initialized) {
+      return;
+    }
+
+    this.entries = [];
+    this.processHooksFromConfig();
+    this.initialized = true;
+
+    debugLogger.log(
+      `Hook registry initialized with ${this.entries.length} hook entries`,
+    );
+  }
+
+  /**
+   * Get all hook entries for a specific event
+   */
+  getHooksForEvent(eventName: HookEventName): HookRegistryEntry[] {
+    if (!this.initialized) {
+      throw new HookRegistryNotInitializedError();
+    }
+
+    return this.entries
+      .filter((entry) => entry.eventName === eventName && entry.enabled)
+      .sort(
+        (a, b) =>
+          this.getSourcePriority(a.source) - this.getSourcePriority(b.source),
+      );
+  }
+
+  /**
+   * Get all registered hooks
+   */
+  getAllHooks(): HookRegistryEntry[] {
+    if (!this.initialized) {
+      throw new HookRegistryNotInitializedError();
+    }
+
+    return [...this.entries];
+  }
+
+  /**
+   * Enable or disable a specific hook
+   */
+  setHookEnabled(hookName: string, enabled: boolean): void {
+    const updated = this.entries.filter((entry) => {
+      const name = this.getHookName(entry);
+      if (name === hookName) {
+        entry.enabled = enabled;
+        return true;
+      }
+      return false;
+    });
+
+    if (updated.length > 0) {
+      debugLogger.log(
+        `${enabled ? 'Enabled' : 'Disabled'} ${updated.length} hook(s) matching "${hookName}"`,
+      );
+    } else {
+      debugLogger.warn(`No hooks found matching "${hookName}"`);
+    }
+  }
+
+  /**
+   * Get hook name for display purposes
+   */
+  private getHookName(entry: HookRegistryEntry): string {
+    return entry.config.command || 'unknown-command';
+  }
+
+  /**
+   * Process hooks from the config that was already loaded by the CLI
+   */
+  private processHooksFromConfig(): void {
+    // Get hooks from the main config (this comes from the merged settings)
+    const configHooks = this.config.getHooks();
+    if (configHooks) {
+      this.processHooksConfiguration(configHooks, ConfigSource.Project);
+    }
+
+    // Get hooks from extensions
+    const extensions = this.config.getExtensions() || [];
+    for (const extension of extensions) {
+      if (extension.isActive && extension.hooks) {
+        this.processHooksConfiguration(
+          extension.hooks,
+          ConfigSource.Extensions,
+        );
+      }
+    }
+  }
+
+  /**
+   * Process hooks configuration and add entries
+   */
+  private processHooksConfiguration(
+    hooksConfig: { [K in HookEventName]?: HookDefinition[] },
+    source: ConfigSource,
+  ): void {
+    for (const [eventName, definitions] of Object.entries(hooksConfig)) {
+      if (!this.isValidEventName(eventName)) {
+        debugLogger.warn(`Invalid hook event name: ${eventName}`);
+        continue;
+      }
+
+      const typedEventName = eventName as HookEventName;
+
+      if (!Array.isArray(definitions)) {
+        debugLogger.warn(
+          `Hook definitions for event "${eventName}" from source "${source}" is not an array. Skipping.`,
+        );
+        continue;
+      }
+
+      for (const definition of definitions) {
+        this.processHookDefinition(definition, typedEventName, source);
+      }
+    }
+  }
+
+  /**
+   * Process a single hook definition
+   */
+  private processHookDefinition(
+    definition: HookDefinition,
+    eventName: HookEventName,
+    source: ConfigSource,
+  ): void {
+    if (
+      !definition ||
+      typeof definition !== 'object' ||
+      !Array.isArray(definition.hooks)
+    ) {
+      debugLogger.warn(
+        `Discarding invalid hook definition for ${eventName} from ${source}:`,
+        definition,
+      );
+      return;
+    }
+
+    for (const hookConfig of definition.hooks) {
+      if (
+        hookConfig &&
+        typeof hookConfig === 'object' &&
+        this.validateHookConfig(hookConfig, eventName, source)
+      ) {
+        this.entries.push({
+          config: hookConfig,
+          source,
+          eventName,
+          matcher: definition.matcher,
+          sequential: definition.sequential,
+          enabled: true,
+        });
+      } else {
+        // Invalid hooks are logged and discarded here, they won't reach HookRunner
+        debugLogger.warn(
+          `Discarding invalid hook configuration for ${eventName} from ${source}:`,
+          hookConfig,
+        );
+      }
+    }
+  }
+
+  /**
+   * Validate a hook configuration
+   */
+  private validateHookConfig(
+    config: HookConfig,
+    eventName: HookEventName,
+    source: ConfigSource,
+  ): boolean {
+    if (!config.type || !['command', 'plugin'].includes(config.type)) {
+      debugLogger.warn(
+        `Invalid hook ${eventName} from ${source} type: ${config.type}`,
+      );
+      return false;
+    }
+
+    if (config.type === 'command' && !config.command) {
+      debugLogger.warn(
+        `Command hook ${eventName} from ${source} missing command field`,
+      );
+      return false;
+    }
+
+    return true;
+  }
+
+  /**
+   * Check if an event name is valid
+   */
+  private isValidEventName(eventName: string): eventName is HookEventName {
+    const validEventNames = Object.values(HookEventName);
+    return validEventNames.includes(eventName as HookEventName);
+  }
+
+  /**
+   * Get source priority (lower number = higher priority)
+   */
+  private getSourcePriority(source: ConfigSource): number {
+    switch (source) {
+      case ConfigSource.Project:
+        return 1;
+      case ConfigSource.User:
+        return 2;
+      case ConfigSource.System:
+        return 3;
+      case ConfigSource.Extensions:
+        return 4;
+      default:
+        return 999;
+    }
+  }
+}