diff --git a/packages/cli/src/ui/commands/memoryCommand.test.ts b/packages/cli/src/ui/commands/memoryCommand.test.ts
index f555a9c925..a1d9642d37 100644
--- a/packages/cli/src/ui/commands/memoryCommand.test.ts
+++ b/packages/cli/src/ui/commands/memoryCommand.test.ts
@@ -182,6 +182,9 @@ describe('memoryCommand', () => {
           include: [],
         }),
         isTrustedFolder: () => false,
+        updateSystemInstructionIfInitialized: vi
+          .fn()
+          .mockResolvedValue(undefined),
       };
 
       mockContext = createMockCommandContext({
diff --git a/packages/cli/src/ui/commands/memoryCommand.ts b/packages/cli/src/ui/commands/memoryCommand.ts
index 61d0ec4467..953a9e7633 100644
--- a/packages/cli/src/ui/commands/memoryCommand.ts
+++ b/packages/cli/src/ui/commands/memoryCommand.ts
@@ -86,6 +86,8 @@ export const memoryCommand: SlashCommand = {
             const { memoryContent, fileCount } =
               await refreshServerHierarchicalMemory(config);
 
+            await config.updateSystemInstructionIfInitialized();
+
             const successMessage =
               memoryContent.length > 0
                 ? `Memory refreshed successfully. Loaded ${memoryContent.length} characters from ${fileCount} file(s).`
diff --git a/packages/core/src/config/config.ts b/packages/core/src/config/config.ts
index c7d1f60edd..6c2a962cfc 100644
--- a/packages/core/src/config/config.ts
+++ b/packages/core/src/config/config.ts
@@ -1020,6 +1020,17 @@ export class Config {
     return this.geminiClient;
   }
 
+  /**
+   * Updates the system instruction with the latest user memory.
+   * Whenever the user memory (GEMINI.md files) is updated.
+   */
+  async updateSystemInstructionIfInitialized(): Promise<void> {
+    const geminiClient = this.getGeminiClient();
+    if (geminiClient?.isInitialized()) {
+      await geminiClient.updateSystemInstruction();
+    }
+  }
+
   getModelRouterService(): ModelRouterService {
     return this.modelRouterService;
   }
diff --git a/packages/core/src/core/client.ts b/packages/core/src/core/client.ts
index 165ce348d5..e2addd0925 100644
--- a/packages/core/src/core/client.ts
+++ b/packages/core/src/core/client.ts
@@ -168,6 +168,16 @@ export class GeminiClient {
     });
   }
 
+  async updateSystemInstruction(): Promise<void> {
+    if (!this.isInitialized()) {
+      return;
+    }
+
+    const userMemory = this.config.getUserMemory();
+    const systemInstruction = getCoreSystemPrompt(this.config, userMemory);
+    this.getChat().setSystemInstruction(systemInstruction);
+  }
+
   async startChat(
     extraHistory?: Content[],
     resumedSessionData?: ResumedSessionData,