diff --git a/packages/cli/src/ui/App.test.tsx b/packages/cli/src/ui/App.test.tsx
index 55e16e0992..7fffa15743 100644
--- a/packages/cli/src/ui/App.test.tsx
+++ b/packages/cli/src/ui/App.test.tsx
@@ -233,6 +233,14 @@ vi.mock('./hooks/useLogger', () => ({
   })),
 }));
 
+vi.mock('./hooks/useInputHistoryStore.js', () => ({
+  useInputHistoryStore: vi.fn(() => ({
+    inputHistory: [],
+    addInput: vi.fn(),
+    initializeFromLogger: vi.fn(),
+  })),
+}));
+
 vi.mock('./hooks/useConsoleMessages.js', () => ({
   useConsoleMessages: vi.fn(() => ({
     consoleMessages: [],
diff --git a/packages/cli/src/ui/App.tsx b/packages/cli/src/ui/App.tsx
index 8cb4eed67c..2783942c2f 100644
--- a/packages/cli/src/ui/App.tsx
+++ b/packages/cli/src/ui/App.tsx
@@ -56,6 +56,7 @@ import { DetailedMessagesDisplay } from './components/DetailedMessagesDisplay.js
 import { HistoryItemDisplay } from './components/HistoryItemDisplay.js';
 import { ContextSummaryDisplay } from './components/ContextSummaryDisplay.js';
 import { useHistory } from './hooks/useHistoryManager.js';
+import { useInputHistoryStore } from './hooks/useInputHistoryStore.js';
 import process from 'node:process';
 import type { EditorType, Config, IdeContext } from '@google/gemini-cli-core';
 import {
@@ -624,7 +625,8 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
     shellModeActive,
   });
 
-  const [userMessages, setUserMessages] = useState<string[]>([]);
+  // Independent input history management (unaffected by /clear)
+  const inputHistoryStore = useInputHistoryStore();
 
   // Stable reference for cancel handler to avoid circular dependency
   const cancelHandlerRef = useRef<() => void>(() => {});
@@ -673,7 +675,7 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
       return;
     }
 
-    const lastUserMessage = userMessages.at(-1);
+    const lastUserMessage = inputHistoryStore.inputHistory.at(-1);
     let textToSet = lastUserMessage || '';
 
     // Append queued messages if any exist
@@ -688,7 +690,7 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
     }
   }, [
     buffer,
-    userMessages,
+    inputHistoryStore.inputHistory,
     getQueuedMessagesText,
     clearQueue,
     pendingHistoryItems,
@@ -697,9 +699,15 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
   // Input handling - queue messages for processing
   const handleFinalSubmit = useCallback(
     (submittedValue: string) => {
+      const trimmedValue = submittedValue.trim();
+      if (trimmedValue.length > 0) {
+        // Add to independent input history
+        inputHistoryStore.addInput(trimmedValue);
+      }
+      // Always add to message queue
       addMessage(submittedValue);
     },
-    [addMessage],
+    [addMessage, inputHistoryStore],
   );
 
   const handleIdePromptComplete = useCallback(
@@ -842,41 +850,10 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
 
   const logger = useLogger(config.storage);
 
+  // Initialize independent input history from logger
   useEffect(() => {
-    const fetchUserMessages = async () => {
-      const pastMessagesRaw = (await logger?.getPreviousUserMessages()) || []; // Newest first
-
-      const currentSessionUserMessages = history
-        .filter(
-          (item): item is HistoryItem & { type: 'user'; text: string } =>
-            item.type === 'user' &&
-            typeof item.text === 'string' &&
-            item.text.trim() !== '',
-        )
-        .map((item) => item.text)
-        .reverse(); // Newest first, to match pastMessagesRaw sorting
-
-      // Combine, with current session messages being more recent
-      const combinedMessages = [
-        ...currentSessionUserMessages,
-        ...pastMessagesRaw,
-      ];
-
-      // Deduplicate consecutive identical messages from the combined list (still newest first)
-      const deduplicatedMessages: string[] = [];
-      if (combinedMessages.length > 0) {
-        deduplicatedMessages.push(combinedMessages[0]); // Add the newest one unconditionally
-        for (let i = 1; i < combinedMessages.length; i++) {
-          if (combinedMessages[i] !== combinedMessages[i - 1]) {
-            deduplicatedMessages.push(combinedMessages[i]);
-          }
-        }
-      }
-      // Reverse to oldest first for useInputHistory
-      setUserMessages(deduplicatedMessages.reverse());
-    };
-    fetchUserMessages();
-  }, [history, logger]);
+    inputHistoryStore.initializeFromLogger(logger);
+  }, [logger, inputHistoryStore]);
 
   const isInputActive =
     (streamingState === StreamingState.Idle ||
@@ -1336,7 +1313,7 @@ const App = ({ config, settings, startupWarnings = [], version }: AppProps) => {
                   inputWidth={inputWidth}
                   suggestionsWidth={suggestionsWidth}
                   onSubmit={handleFinalSubmit}
-                  userMessages={userMessages}
+                  userMessages={inputHistoryStore.inputHistory}
                   onClearScreen={handleClearScreen}
                   config={config}
                   slashCommands={slashCommands}
diff --git a/packages/cli/src/ui/hooks/useInputHistoryStore.test.ts b/packages/cli/src/ui/hooks/useInputHistoryStore.test.ts
new file mode 100644
index 0000000000..5404cefc02
--- /dev/null
+++ b/packages/cli/src/ui/hooks/useInputHistoryStore.test.ts
@@ -0,0 +1,301 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { act, renderHook } from '@testing-library/react';
+import { vi, describe, it, expect, beforeEach } from 'vitest';
+import { useInputHistoryStore } from './useInputHistoryStore.js';
+
+describe('useInputHistoryStore', () => {
+  beforeEach(() => {
+    vi.clearAllMocks();
+  });
+
+  it('should initialize with empty input history', () => {
+    const { result } = renderHook(() => useInputHistoryStore());
+
+    expect(result.current.inputHistory).toEqual([]);
+  });
+
+  it('should add input to history', () => {
+    const { result } = renderHook(() => useInputHistoryStore());
+
+    act(() => {
+      result.current.addInput('test message 1');
+    });
+
+    expect(result.current.inputHistory).toEqual(['test message 1']);
+
+    act(() => {
+      result.current.addInput('test message 2');
+    });
+
+    expect(result.current.inputHistory).toEqual([
+      'test message 1',
+      'test message 2',
+    ]);
+  });
+
+  it('should not add empty or whitespace-only inputs', () => {
+    const { result } = renderHook(() => useInputHistoryStore());
+
+    act(() => {
+      result.current.addInput('');
+    });
+
+    expect(result.current.inputHistory).toEqual([]);
+
+    act(() => {
+      result.current.addInput('   ');
+    });
+
+    expect(result.current.inputHistory).toEqual([]);
+  });
+
+  it('should deduplicate consecutive identical messages', () => {
+    const { result } = renderHook(() => useInputHistoryStore());
+
+    act(() => {
+      result.current.addInput('test message');
+    });
+
+    act(() => {
+      result.current.addInput('test message'); // Same as previous
+    });
+
+    expect(result.current.inputHistory).toEqual(['test message']);
+
+    act(() => {
+      result.current.addInput('different message');
+    });
+
+    act(() => {
+      result.current.addInput('test message'); // Same as first, but not consecutive
+    });
+
+    expect(result.current.inputHistory).toEqual([
+      'test message',
+      'different message',
+      'test message',
+    ]);
+  });
+
+  it('should initialize from logger successfully', async () => {
+    const mockLogger = {
+      getPreviousUserMessages: vi
+        .fn()
+        .mockResolvedValue(['newest', 'middle', 'oldest']),
+    };
+
+    const { result } = renderHook(() => useInputHistoryStore());
+
+    await act(async () => {
+      await result.current.initializeFromLogger(mockLogger);
+    });
+
+    // Should reverse the order to oldest first
+    expect(result.current.inputHistory).toEqual(['oldest', 'middle', 'newest']);
+    expect(mockLogger.getPreviousUserMessages).toHaveBeenCalledTimes(1);
+  });
+
+  it('should handle logger initialization failure gracefully', async () => {
+    const mockLogger = {
+      getPreviousUserMessages: vi
+        .fn()
+        .mockRejectedValue(new Error('Logger error')),
+    };
+
+    const consoleSpy = vi.spyOn(console, 'warn').mockImplementation(() => {});
+
+    const { result } = renderHook(() => useInputHistoryStore());
+
+    await act(async () => {
+      await result.current.initializeFromLogger(mockLogger);
+    });
+
+    expect(result.current.inputHistory).toEqual([]);
+    expect(consoleSpy).toHaveBeenCalledWith(
+      'Failed to initialize input history from logger:',
+      expect.any(Error),
+    );
+
+    consoleSpy.mockRestore();
+  });
+
+  it('should initialize only once', async () => {
+    const mockLogger = {
+      getPreviousUserMessages: vi
+        .fn()
+        .mockResolvedValue(['message1', 'message2']),
+    };
+
+    const { result } = renderHook(() => useInputHistoryStore());
+
+    // Call initializeFromLogger twice
+    await act(async () => {
+      await result.current.initializeFromLogger(mockLogger);
+    });
+
+    await act(async () => {
+      await result.current.initializeFromLogger(mockLogger);
+    });
+
+    // Should be called only once
+    expect(mockLogger.getPreviousUserMessages).toHaveBeenCalledTimes(1);
+    expect(result.current.inputHistory).toEqual(['message2', 'message1']);
+  });
+
+  it('should handle null logger gracefully', async () => {
+    const { result } = renderHook(() => useInputHistoryStore());
+
+    await act(async () => {
+      await result.current.initializeFromLogger(null);
+    });
+
+    expect(result.current.inputHistory).toEqual([]);
+  });
+
+  it('should trim input before adding to history', () => {
+    const { result } = renderHook(() => useInputHistoryStore());
+
+    act(() => {
+      result.current.addInput('  test message  ');
+    });
+
+    expect(result.current.inputHistory).toEqual(['test message']);
+  });
+
+  describe('deduplication logic from previous implementation', () => {
+    it('should deduplicate consecutive messages from past sessions during initialization', async () => {
+      const mockLogger = {
+        getPreviousUserMessages: vi
+          .fn()
+          .mockResolvedValue([
+            'message1',
+            'message1',
+            'message2',
+            'message2',
+            'message3',
+          ]), // newest first with duplicates
+      };
+
+      const { result } = renderHook(() => useInputHistoryStore());
+
+      await act(async () => {
+        await result.current.initializeFromLogger(mockLogger);
+      });
+
+      // Should deduplicate consecutive messages and reverse to oldest first
+      expect(result.current.inputHistory).toEqual([
+        'message3',
+        'message2',
+        'message1',
+      ]);
+    });
+
+    it('should deduplicate across session boundaries', async () => {
+      const mockLogger = {
+        getPreviousUserMessages: vi.fn().mockResolvedValue(['old2', 'old1']), // newest first
+      };
+
+      const { result } = renderHook(() => useInputHistoryStore());
+
+      // Initialize with past session
+      await act(async () => {
+        await result.current.initializeFromLogger(mockLogger);
+      });
+
+      // Add current session inputs
+      act(() => {
+        result.current.addInput('old2'); // Same as last past session message
+      });
+
+      // Should deduplicate across session boundary
+      expect(result.current.inputHistory).toEqual(['old1', 'old2']);
+
+      act(() => {
+        result.current.addInput('new1');
+      });
+
+      expect(result.current.inputHistory).toEqual(['old1', 'old2', 'new1']);
+    });
+
+    it('should preserve non-consecutive duplicates', async () => {
+      const mockLogger = {
+        getPreviousUserMessages: vi
+          .fn()
+          .mockResolvedValue(['message2', 'message1', 'message2']), // newest first with non-consecutive duplicate
+      };
+
+      const { result } = renderHook(() => useInputHistoryStore());
+
+      await act(async () => {
+        await result.current.initializeFromLogger(mockLogger);
+      });
+
+      // Non-consecutive duplicates should be preserved
+      expect(result.current.inputHistory).toEqual([
+        'message2',
+        'message1',
+        'message2',
+      ]);
+    });
+
+    it('should handle complex deduplication with current session', () => {
+      const { result } = renderHook(() => useInputHistoryStore());
+
+      // Add multiple messages with duplicates
+      act(() => {
+        result.current.addInput('hello');
+      });
+      act(() => {
+        result.current.addInput('hello'); // consecutive duplicate
+      });
+      act(() => {
+        result.current.addInput('world');
+      });
+      act(() => {
+        result.current.addInput('world'); // consecutive duplicate
+      });
+      act(() => {
+        result.current.addInput('hello'); // non-consecutive duplicate
+      });
+
+      // Should have deduplicated consecutive ones
+      expect(result.current.inputHistory).toEqual(['hello', 'world', 'hello']);
+    });
+
+    it('should maintain oldest-first order in final output', async () => {
+      const mockLogger = {
+        getPreviousUserMessages: vi
+          .fn()
+          .mockResolvedValue(['newest', 'middle', 'oldest']), // newest first
+      };
+
+      const { result } = renderHook(() => useInputHistoryStore());
+
+      await act(async () => {
+        await result.current.initializeFromLogger(mockLogger);
+      });
+
+      // Add current session messages
+      act(() => {
+        result.current.addInput('current1');
+      });
+      act(() => {
+        result.current.addInput('current2');
+      });
+
+      // Should maintain oldest-first order
+      expect(result.current.inputHistory).toEqual([
+        'oldest',
+        'middle',
+        'newest',
+        'current1',
+        'current2',
+      ]);
+    });
+  });
+});
diff --git a/packages/cli/src/ui/hooks/useInputHistoryStore.ts b/packages/cli/src/ui/hooks/useInputHistoryStore.ts
new file mode 100644
index 0000000000..86e7cd3960
--- /dev/null
+++ b/packages/cli/src/ui/hooks/useInputHistoryStore.ts
@@ -0,0 +1,112 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { useState, useCallback } from 'react';
+
+interface Logger {
+  getPreviousUserMessages(): Promise<string[]>;
+}
+
+export interface UseInputHistoryStoreReturn {
+  inputHistory: string[];
+  addInput: (input: string) => void;
+  initializeFromLogger: (logger: Logger | null) => Promise<void>;
+}
+
+/**
+ * Hook for independently managing input history.
+ * Completely separated from chat history and unaffected by /clear commands.
+ */
+export function useInputHistoryStore(): UseInputHistoryStoreReturn {
+  const [inputHistory, setInputHistory] = useState<string[]>([]);
+  const [_pastSessionMessages, setPastSessionMessages] = useState<string[]>([]);
+  const [_currentSessionMessages, setCurrentSessionMessages] = useState<
+    string[]
+  >([]);
+  const [isInitialized, setIsInitialized] = useState(false);
+
+  /**
+   * Recalculate the complete input history from past and current sessions.
+   * Applies the same deduplication logic as the previous implementation.
+   */
+  const recalculateHistory = useCallback(
+    (currentSession: string[], pastSession: string[]) => {
+      // Combine current session (newest first) + past session (newest first)
+      const combinedMessages = [...currentSession, ...pastSession];
+
+      // Deduplicate consecutive identical messages (same algorithm as before)
+      const deduplicatedMessages: string[] = [];
+      if (combinedMessages.length > 0) {
+        deduplicatedMessages.push(combinedMessages[0]); // Add the newest one unconditionally
+        for (let i = 1; i < combinedMessages.length; i++) {
+          if (combinedMessages[i] !== combinedMessages[i - 1]) {
+            deduplicatedMessages.push(combinedMessages[i]);
+          }
+        }
+      }
+
+      // Reverse to oldest first for useInputHistory
+      setInputHistory(deduplicatedMessages.reverse());
+    },
+    [],
+  );
+
+  /**
+   * Initialize input history from logger with past session data.
+   * Executed only once at app startup.
+   */
+  const initializeFromLogger = useCallback(
+    async (logger: Logger | null) => {
+      if (isInitialized || !logger) return;
+
+      try {
+        const pastMessages = (await logger.getPreviousUserMessages()) || [];
+        setPastSessionMessages(pastMessages); // Store as newest first
+        recalculateHistory([], pastMessages);
+        setIsInitialized(true);
+      } catch (error) {
+        // Start with empty history even if logger initialization fails
+        console.warn('Failed to initialize input history from logger:', error);
+        setPastSessionMessages([]);
+        recalculateHistory([], []);
+        setIsInitialized(true);
+      }
+    },
+    [isInitialized, recalculateHistory],
+  );
+
+  /**
+   * Add new input to history.
+   * Recalculates the entire history with deduplication.
+   */
+  const addInput = useCallback(
+    (input: string) => {
+      const trimmedInput = input.trim();
+      if (!trimmedInput) return; // Filter empty/whitespace-only inputs
+
+      setCurrentSessionMessages((prevCurrent) => {
+        const newCurrentSession = [...prevCurrent, trimmedInput];
+
+        setPastSessionMessages((prevPast) => {
+          recalculateHistory(
+            newCurrentSession.slice().reverse(), // Convert to newest first
+            prevPast,
+          );
+          return prevPast; // No change to past messages
+        });
+
+        return newCurrentSession;
+      });
+    },
+    [recalculateHistory],
+  );
+
+  return {
+    inputHistory,
+    addInput,
+    initializeFromLogger,
+  };
+}