diff --git a/src/core/file/fileSearch.ts b/src/core/file/fileSearch.ts
index 8bf343c63..8e3e885e4 100644
--- a/src/core/file/fileSearch.ts
+++ b/src/core/file/fileSearch.ts
@@ -42,6 +42,21 @@ const findEmptyDirectories = async (
   return emptyDirs;
 };
 
+// Check if a path is a git worktree reference file
+const isGitWorktreeRef = async (gitPath: string): Promise<boolean> => {
+  try {
+    const stats = await fs.stat(gitPath);
+    if (!stats.isFile()) {
+      return false;
+    }
+
+    const content = await fs.readFile(gitPath, 'utf8');
+    return content.startsWith('gitdir:');
+  } catch {
+    return false;
+  }
+};
+
 // Get all file paths considering the config
 export const searchFiles = async (rootDir: string, config: RepomixConfigMerged): Promise<FileSearchResult> => {
   // First check directory permissions
@@ -66,9 +81,24 @@ export const searchFiles = async (rootDir: string, config: RepomixConfigMerged):
     logger.trace('Ignore patterns:', ignorePatterns);
     logger.trace('Ignore file patterns:', ignoreFilePatterns);
 
+    // Check if .git is a worktree reference
+    const gitPath = path.join(rootDir, '.git');
+    const isWorktree = await isGitWorktreeRef(gitPath);
+
+    // Modify ignore patterns for git worktree
+    const adjustedIgnorePatterns = [...ignorePatterns];
+    if (isWorktree) {
+      // Remove '.git/**' pattern and add '.git' to ignore the reference file
+      const gitIndex = adjustedIgnorePatterns.indexOf('.git/**');
+      if (gitIndex !== -1) {
+        adjustedIgnorePatterns.splice(gitIndex, 1);
+        adjustedIgnorePatterns.push('.git');
+      }
+    }
+
     const filePaths = await globby(includePatterns, {
       cwd: rootDir,
-      ignore: [...ignorePatterns],
+      ignore: [...adjustedIgnorePatterns],
       ignoreFiles: [...ignoreFilePatterns],
       onlyFiles: true,
       absolute: false,
@@ -89,7 +119,7 @@ export const searchFiles = async (rootDir: string, config: RepomixConfigMerged):
     if (config.output.includeEmptyDirectories) {
       const directories = await globby(includePatterns, {
         cwd: rootDir,
-        ignore: [...ignorePatterns],
+        ignore: [...adjustedIgnorePatterns],
         ignoreFiles: [...ignoreFilePatterns],
         onlyDirectories: true,
         absolute: false,
@@ -97,7 +127,7 @@ export const searchFiles = async (rootDir: string, config: RepomixConfigMerged):
         followSymbolicLinks: false,
       });
 
-      emptyDirPaths = await findEmptyDirectories(rootDir, directories, ignorePatterns);
+      emptyDirPaths = await findEmptyDirectories(rootDir, directories, adjustedIgnorePatterns);
     }
 
     logger.trace(`Filtered ${filePaths.length} files`);
diff --git a/tests/core/file/fileSearch.test.ts b/tests/core/file/fileSearch.test.ts
index 65b9e227d..ab89b7142 100644
--- a/tests/core/file/fileSearch.test.ts
+++ b/tests/core/file/fileSearch.test.ts
@@ -1,3 +1,4 @@
+import type { Stats } from 'node:fs';
 import * as fs from 'node:fs/promises';
 import path from 'node:path';
 import process from 'node:process';
@@ -272,5 +273,73 @@ node_modules
       expect(result.filePaths).toContain('root/subdir/ignored.js');
       expect(result.emptyDirPaths).toEqual([]);
     });
+
+    test('should handle git worktree correctly', async () => {
+      // Mock .git file content for worktree
+      const gitWorktreeContent = 'gitdir: /path/to/main/repo/.git/worktrees/feature-branch';
+
+      // Mock fs.stat and fs.readFile for .git file
+      vi.mocked(fs.stat).mockResolvedValue({
+        isFile: () => true,
+      } as Stats);
+      vi.mocked(fs.readFile).mockResolvedValue(gitWorktreeContent);
+
+      // Mock globby to return some test files
+      vi.mocked(globby).mockResolvedValue(['file1.js', 'file2.js']);
+
+      const mockConfig = createMockConfig({
+        ignore: {
+          useGitignore: true,
+          useDefaultPatterns: true,
+          customPatterns: [],
+        },
+      });
+
+      const result = await searchFiles('/test/dir', mockConfig);
+
+      // Check that globby was called with correct ignore patterns
+      const globbyCall = vi.mocked(globby).mock.calls[0];
+      const ignorePatterns = globbyCall[1]?.ignore as string[];
+
+      // Verify .git file (not directory) is in ignore patterns
+      expect(ignorePatterns).toContain('.git');
+      // Verify .git/** is not in ignore patterns
+      expect(ignorePatterns).not.toContain('.git/**');
+
+      // Verify the files were returned correctly
+      expect(result.filePaths).toEqual(['file1.js', 'file2.js']);
+    });
+
+    test('should handle regular git repository correctly', async () => {
+      // Mock .git as a directory
+      vi.mocked(fs.stat).mockResolvedValue({
+        isFile: () => false,
+      } as Stats);
+
+      // Mock globby to return some test files
+      vi.mocked(globby).mockResolvedValue(['file1.js', 'file2.js']);
+
+      const mockConfig = createMockConfig({
+        ignore: {
+          useGitignore: true,
+          useDefaultPatterns: true,
+          customPatterns: [],
+        },
+      });
+
+      const result = await searchFiles('/test/dir', mockConfig);
+
+      // Check that globby was called with correct ignore patterns
+      const globbyCall = vi.mocked(globby).mock.calls[0];
+      const ignorePatterns = globbyCall[1]?.ignore as string[];
+
+      // Verify .git/** is in ignore patterns for regular git repos
+      expect(ignorePatterns).toContain('.git/**');
+      // Verify just .git is not in ignore patterns
+      expect(ignorePatterns).not.toContain('.git');
+
+      // Verify the files were returned correctly
+      expect(result.filePaths).toEqual(['file1.js', 'file2.js']);
+    });
   });
 });