diff --git a/src/core/file/fileSearch.ts b/src/core/file/fileSearch.ts
index 46a994a5..60deb32a 100644
--- a/src/core/file/fileSearch.ts
+++ b/src/core/file/fileSearch.ts
@@ -3,8 +3,19 @@ import type { RepomixConfigMerged } from '../../config/configTypes.js';
 import { defaultIgnoreList } from '../../config/defaultIgnore.js';
 import { logger } from '../../shared/logger.js';
 import { sortPaths } from './filePathSort.js';
+import { PermissionError, checkDirectoryPermissions } from './permissionCheck.js';
 
 export const searchFiles = async (rootDir: string, config: RepomixConfigMerged): Promise<string[]> => {
+  // First check directory permissions
+  const permissionCheck = await checkDirectoryPermissions(rootDir);
+
+  if (!permissionCheck.hasPermission) {
+    if (permissionCheck.error instanceof PermissionError) {
+      throw permissionCheck.error;
+    }
+    throw new Error(`Cannot access directory ${rootDir}: ${permissionCheck.error?.message}`);
+  }
+
   const includePatterns = config.include.length > 0 ? config.include : ['**/*'];
 
   try {
@@ -25,6 +36,15 @@ export const searchFiles = async (rootDir: string, config: RepomixConfigMerged):
       absolute: false,
       dot: true,
       followSymbolicLinks: false,
+    }).catch((error) => {
+      // Handle EPERM errors specifically
+      if (error.code === 'EPERM' || error.code === 'EACCES') {
+        throw new PermissionError(
+          'Permission denied while scanning directory. Please check folder access permissions for your terminal app.',
+          rootDir,
+        );
+      }
+      throw error;
     });
 
     logger.trace(`Filtered ${filePaths.length} files`);
@@ -32,10 +52,16 @@ export const searchFiles = async (rootDir: string, config: RepomixConfigMerged):
 
     return sortedPaths;
   } catch (error: unknown) {
+    // Re-throw PermissionError as is
+    if (error instanceof PermissionError) {
+      throw error;
+    }
+
     if (error instanceof Error) {
       logger.error('Error filtering files:', error.message);
       throw new Error(`Failed to filter files in directory ${rootDir}. Reason: ${error.message}`);
     }
+
     logger.error('An unexpected error occurred:', error);
     throw new Error('An unexpected error occurred while filtering files.');
   }
diff --git a/src/core/file/permissionCheck.ts b/src/core/file/permissionCheck.ts
new file mode 100644
index 00000000..d2ea53ff
--- /dev/null
+++ b/src/core/file/permissionCheck.ts
@@ -0,0 +1,115 @@
+import { constants, access } from 'node:fs';
+import * as fs from 'node:fs/promises';
+import { platform } from 'node:os';
+import { promisify } from 'node:util';
+import { logger } from '../../shared/logger.js';
+
+const asyncAccess = promisify(access);
+
+export interface PermissionCheckResult {
+  hasPermission: boolean;
+  error?: Error;
+  details?: {
+    read?: boolean;
+    write?: boolean;
+    execute?: boolean;
+  };
+}
+
+export class PermissionError extends Error {
+  constructor(
+    message: string,
+    public readonly path: string,
+    public readonly code?: string,
+  ) {
+    super(message);
+    this.name = 'PermissionError';
+  }
+}
+
+export async function checkDirectoryPermissions(dirPath: string): Promise<PermissionCheckResult> {
+  try {
+    // First try to read directory contents
+    await fs.readdir(dirPath);
+
+    // Check specific permissions
+    const details = {
+      read: false,
+      write: false,
+      execute: false,
+    };
+
+    try {
+      await asyncAccess(dirPath, constants.R_OK);
+      details.read = true;
+    } catch {}
+
+    try {
+      await asyncAccess(dirPath, constants.W_OK);
+      details.write = true;
+    } catch {}
+
+    try {
+      await asyncAccess(dirPath, constants.X_OK);
+      details.execute = true;
+    } catch {}
+
+    const hasAllPermissions = details.read && details.write && details.execute;
+
+    if (!hasAllPermissions) {
+      return {
+        hasPermission: false,
+        details,
+      };
+    }
+
+    return {
+      hasPermission: true,
+      details,
+    };
+  } catch (error) {
+    if (error instanceof Error && 'code' in error) {
+      switch (error.code) {
+        case 'EPERM':
+        case 'EACCES':
+        case 'EISDIR':
+          return {
+            hasPermission: false,
+            error: new PermissionError(getMacOSPermissionMessage(dirPath, error.code), dirPath, error.code),
+          };
+        default:
+          logger.debug('Directory permission check error:', error);
+          return {
+            hasPermission: false,
+            error: error as Error,
+          };
+      }
+    }
+    return {
+      hasPermission: false,
+      error: error instanceof Error ? error : new Error(String(error)),
+    };
+  }
+}
+
+function getMacOSPermissionMessage(dirPath: string, errorCode?: string): string {
+  if (platform() === 'darwin') {
+    return `Permission denied: Cannot access '${dirPath}', error code: ${errorCode}.
+
+This error often occurs when macOS security restrictions prevent access to the directory.
+To fix this:
+
+1. Open System Settings
+2. Navigate to Privacy & Security > Files and Folders
+3. Find your terminal app (Terminal.app, iTerm2, VS Code, etc.)
+4. Grant necessary folder access permissions
+
+If your terminal app is not listed:
+- Try running repomix command again
+- When prompted by macOS, click "Allow"
+- Restart your terminal app if needed
+`;
+  }
+
+  return `Permission denied: Cannot access '${dirPath}'`;
+}