diff --git a/packages/cli/README.md b/packages/cli/README.md
index 3f90e4f..502645f 100644
--- a/packages/cli/README.md
+++ b/packages/cli/README.md
@@ -75,6 +75,9 @@ mycoder config get githubMode
 # Set a configuration value
 mycoder config set githubMode true
 
+# Reset a configuration value to its default
+mycoder config clear customPrompt
+
 # Configure model provider and model name
 mycoder config set modelProvider openai
 mycoder config set modelName gpt-4o-2024-05-13
diff --git a/packages/cli/src/commands/config.ts b/packages/cli/src/commands/config.ts
index 53ee5ad..190c252 100644
--- a/packages/cli/src/commands/config.ts
+++ b/packages/cli/src/commands/config.ts
@@ -2,13 +2,17 @@ import chalk from 'chalk';
 import { Logger } from 'mycoder-agent';
 
 import { SharedOptions } from '../options.js';
-import { getConfig, updateConfig } from '../settings/config.js';
+import {
+  getConfig,
+  getDefaultConfig,
+  updateConfig,
+} from '../settings/config.js';
 import { nameToLogIndex } from '../utils/nameToLogIndex.js';
 
 import type { CommandModule, ArgumentsCamelCase } from 'yargs';
 
 export interface ConfigOptions extends SharedOptions {
-  command: 'get' | 'set' | 'list';
+  command: 'get' | 'set' | 'list' | 'clear';
   key?: string;
   value?: string;
 }
@@ -20,7 +24,7 @@ export const command: CommandModule<SharedOptions, ConfigOptions> = {
     return yargs
       .positional('command', {
         describe: 'Config command to run',
-        choices: ['get', 'set', 'list'],
+        choices: ['get', 'set', 'list', 'clear'],
         type: 'string',
         demandOption: true,
       })
@@ -37,7 +41,11 @@ export const command: CommandModule<SharedOptions, ConfigOptions> = {
         '$0 config get githubMode',
         'Get the value of githubMode setting',
       )
-      .example('$0 config set githubMode true', 'Enable GitHub mode') as any; // eslint-disable-line @typescript-eslint/no-explicit-any
+      .example('$0 config set githubMode true', 'Enable GitHub mode')
+      .example(
+        '$0 config clear customPrompt',
+        'Reset customPrompt to default value',
+      ) as any; // eslint-disable-line @typescript-eslint/no-explicit-any
   },
   handler: async (argv: ArgumentsCamelCase<ConfigOptions>) => {
     const logger = new Logger({
@@ -50,8 +58,16 @@ export const command: CommandModule<SharedOptions, ConfigOptions> = {
     // Handle 'list' command
     if (argv.command === 'list') {
       logger.info('Current configuration:');
+      const defaultConfig = getDefaultConfig();
       Object.entries(config).forEach(([key, value]) => {
-        logger.info(`  ${key}: ${chalk.green(value)}`);
+        const isDefault =
+          JSON.stringify(value) ===
+          JSON.stringify(defaultConfig[key as keyof typeof defaultConfig]);
+        const valueDisplay = chalk.green(value);
+        const statusIndicator = isDefault
+          ? chalk.dim(' (default)')
+          : chalk.blue(' (custom)');
+        logger.info(`  ${key}: ${valueDisplay}${statusIndicator}`);
       });
       return;
     }
@@ -116,8 +132,51 @@ export const command: CommandModule<SharedOptions, ConfigOptions> = {
       return;
     }
 
+    // Handle 'clear' command
+    if (argv.command === 'clear') {
+      if (!argv.key) {
+        logger.error('Key is required for clear command');
+        return;
+      }
+
+      const defaultConfig = getDefaultConfig();
+
+      // Check if the key exists in the config
+      if (!(argv.key in config)) {
+        logger.error(`Configuration key '${argv.key}' not found`);
+        return;
+      }
+
+      // Check if the key exists in the default config
+      if (!(argv.key in defaultConfig)) {
+        logger.error(
+          `Configuration key '${argv.key}' does not have a default value`,
+        );
+        return;
+      }
+
+      // Get the current config, create a new object without the specified key
+      const currentConfig = getConfig();
+      const { [argv.key]: _, ...newConfig } = currentConfig as Record<
+        string,
+        any
+      >;
+
+      // Update the config file with the new object
+      updateConfig(newConfig);
+
+      // Get the default value that will now be used
+      const defaultValue =
+        defaultConfig[argv.key as keyof typeof defaultConfig];
+
+      logger.info(
+        `Cleared ${argv.key}, now using default value: ${chalk.green(defaultValue)}`,
+      );
+      return;
+    }
+
     // If command not recognized
     logger.error(`Unknown config command: ${argv.command}`);
-    logger.info('Available commands: get, set, list');
+    logger.info('Available commands: get, set, list, clear');
   },
 };
diff --git a/packages/cli/src/settings/config.ts b/packages/cli/src/settings/config.ts
index 30cd925..87a4f7d 100644
--- a/packages/cli/src/settings/config.ts
+++ b/packages/cli/src/settings/config.ts
@@ -24,6 +24,11 @@ const defaultConfig = {
 
 export type Config = typeof defaultConfig;
 
+// Export the default config for use in other functions
+export const getDefaultConfig = (): Config => {
+  return { ...defaultConfig };
+};
+
 export const getConfig = (): Config => {
   if (!fs.existsSync(configFile)) {
     return defaultConfig;
diff --git a/packages/cli/tests/commands/config.test.ts b/packages/cli/tests/commands/config.test.ts
index 3071a14..d07ff31 100644
--- a/packages/cli/tests/commands/config.test.ts
+++ b/packages/cli/tests/commands/config.test.ts
@@ -2,11 +2,16 @@ import { Logger } from 'mycoder-agent';
 import { beforeEach, afterEach, describe, expect, it, vi } from 'vitest';
 
 import { command } from '../../src/commands/config.js';
-import { getConfig, updateConfig } from '../../src/settings/config.js';
+import {
+  getConfig,
+  getDefaultConfig,
+  updateConfig,
+} from '../../src/settings/config.js';
 
 // Mock dependencies
 vi.mock('../../src/settings/config.js', () => ({
   getConfig: vi.fn(),
+  getDefaultConfig: vi.fn(),
   updateConfig: vi.fn(),
 }));
 
@@ -39,6 +44,10 @@ describe.skip('Config Command', () => {
     };
     vi.mocked(Logger).mockImplementation(() => mockLogger as unknown as Logger);
     vi.mocked(getConfig).mockReturnValue({ githubMode: false });
+    vi.mocked(getDefaultConfig).mockReturnValue({
+      githubMode: false,
+      customPrompt: '',
+    });
     vi.mocked(updateConfig).mockImplementation((config) => ({
       githubMode: false,
       ...config,
@@ -150,4 +159,87 @@ describe.skip('Config Command', () => {
       expect.stringContaining('Unknown config command'),
     );
   });
+
+  it('should list all configuration values with default indicators', async () => {
+    // Mock getConfig to return a mix of default and custom values
+    vi.mocked(getConfig).mockReturnValue({
+      githubMode: false, // default value
+      customPrompt: 'custom value', // custom value
+    });
+
+    // Mock getDefaultConfig to return the default values
+    vi.mocked(getDefaultConfig).mockReturnValue({
+      githubMode: false,
+      customPrompt: '',
+    });
+
+    await command.handler!({
+      _: ['config', 'config', 'list'],
+      logLevel: 'info',
+      interactive: false,
+      command: 'list',
+    } as any);
+
+    expect(getConfig).toHaveBeenCalled();
+    expect(getDefaultConfig).toHaveBeenCalled();
+    expect(mockLogger.info).toHaveBeenCalledWith('Current configuration:');
+
+    // Check for default indicator
+    expect(mockLogger.info).toHaveBeenCalledWith(
+      expect.stringContaining('githubMode') &&
+        expect.stringContaining('(default)'),
+    );
+
+    // Check for custom indicator
+    expect(mockLogger.info).toHaveBeenCalledWith(
+      expect.stringContaining('customPrompt') &&
+        expect.stringContaining('(custom)'),
+    );
+  });
+
+  it('should clear a configuration value', async () => {
+    await command.handler!({
+      _: ['config', 'config', 'clear', 'customPrompt'],
+      logLevel: 'info',
+      interactive: false,
+      command: 'clear',
+      key: 'customPrompt',
+    } as any);
+
+    // Verify updateConfig was called with an object that doesn't include the key
+    expect(updateConfig).toHaveBeenCalled();
+
+    // Verify success message
+    expect(mockLogger.info).toHaveBeenCalledWith(
+      expect.stringContaining('Cleared customPrompt'),
+    );
+  });
+
+  it('should handle missing key for clear command', async () => {
+    await command.handler!({
+      _: ['config', 'config', 'clear'],
+      logLevel: 'info',
+      interactive: false,
+      command: 'clear',
+      key: undefined,
+    } as any);
+
+    expect(mockLogger.error).toHaveBeenCalledWith(
+      expect.stringContaining('Key is required'),
+    );
+  });
+
+  it('should handle non-existent key for clear command', async () => {
+    await command.handler!({
+      _: ['config', 'config', 'clear', 'nonExistentKey'],
+      logLevel: 'info',
+      interactive: false,
+      command: 'clear',
+      key: 'nonExistentKey',
+    } as any);
+
+    expect(mockLogger.error).toHaveBeenCalledWith(
+      expect.stringContaining('not found'),
+    );
+  });
 });