diff --git a/packages/core/src/tools/memoryTool.test.ts b/packages/core/src/tools/memoryTool.test.ts
index dcc9a14333..f050c7a0d9 100644
--- a/packages/core/src/tools/memoryTool.test.ts
+++ b/packages/core/src/tools/memoryTool.test.ts
@@ -86,8 +86,8 @@ describe('MemoryTool', () => {
       const newName = 'CUSTOM_CONTEXT.md';
       setGeminiMdFilename(newName);
       expect(getAllGeminiMdFilenames()).toEqual([
-        DEFAULT_CONTEXT_FILENAME,
         newName,
+        DEFAULT_CONTEXT_FILENAME,
       ]);
     });
 
@@ -104,8 +104,8 @@ describe('MemoryTool', () => {
       const newNames = ['CUSTOM_CONTEXT.md', 'ANOTHER_CONTEXT.md'];
       setGeminiMdFilename(newNames);
       expect(getAllGeminiMdFilenames()).toEqual([
-        DEFAULT_CONTEXT_FILENAME,
         ...newNames,
+        DEFAULT_CONTEXT_FILENAME,
       ]);
     });
 
@@ -115,8 +115,8 @@ describe('MemoryTool', () => {
 
       setGeminiMdFilename(['NEW.md', 'NEW.md']);
       expect(getAllGeminiMdFilenames()).toEqual([
-        DEFAULT_CONTEXT_FILENAME,
         'NEW.md',
+        DEFAULT_CONTEXT_FILENAME,
       ]);
     });
   });
diff --git a/packages/core/src/tools/memoryTool.ts b/packages/core/src/tools/memoryTool.ts
index c9335b3594..923082fa02 100644
--- a/packages/core/src/tools/memoryTool.ts
+++ b/packages/core/src/tools/memoryTool.ts
@@ -49,8 +49,15 @@ export function setGeminiMdFilename(newFilename: string | string[]): void {
   for (const filename of filenames) {
     const trimmed = filename.trim();
     if (trimmed !== '') {
-      const safeFilename = path.basename(trimmed);
-      next.add(safeFilename);
+      const normalized = path.normalize(trimmed);
+      // Sanitize to prevent path traversal while allowing subdirectories
+      if (
+        !path.isAbsolute(normalized) &&
+        !normalized.startsWith('..') &&
+        normalized !== '.'
+      ) {
+        next.add(normalized);
+      }
     }
   }
 
@@ -74,7 +81,16 @@ export function resetGeminiMdFilename(
   filename: string | string[] = DEFAULT_CONTEXT_FILENAME,
 ): void {
   const filenames = Array.isArray(filename) ? filename : [filename];
-  const cleaned = filenames.map((f) => path.basename(f.trim())).filter((f) => f !== '');
+  const cleaned = Array.from(
+    new Set(
+      filenames
+        .map((f) => path.normalize(f.trim()))
+        .filter(
+          (f) =>
+            f !== '' && f !== '.' && !f.startsWith('..') && !path.isAbsolute(f),
+        ),
+    ),
+  );
 
   if (cleaned.length === 0) {
     currentGeminiMdFilename = DEFAULT_CONTEXT_FILENAME;