GitHub MCP Server: Complete Guide to AI-Powered Repository Management

TL;DR - GitHub MCP Quick Start

Most popular MCP server - Connect your AI to GitHub for repository management.

🆕 December 2025: GitHub Copilot Extensions are being deprecated in favor of MCP servers. MCP is now the standard for extending GitHub Copilot! For an introduction to MCP, see the MCP Introduction guide.

Quick Setup:

{
  "mcpServers": {
    "github": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "ghp_xxxxxxxxxxxx"
      }
    }
  }
}

What you can do:

• 🔍 Search: Find repos, code, issues, users
• 📝 Issues: Create, update, close, comment, assign
• 🔀 Pull Requests: Create, review, merge, comment
• 📁 Files: Read, create, update files in repos
• 🌿 Branches: Create, list, manage branches
• 🍴 Forks: Fork any public repository

Example conversation:

You: Create an issue in my-org/my-repo titled "Bug: Login fails on Safari" 
     with details about the error

Claude: I've created issue #142 in my-org/my-repo:
        "Bug: Login fails on Safari"
        URL: https://github.com/my-org/my-repo/issues/142

💡 Full guide below with all 20+ tools, workflows, and example prompts.

Why GitHub MCP is #1

GitHub MCP Server is the most downloaded MCP server for good reason:

🚨 Important (2025): GitHub is deprecating Copilot Extensions (GitHub Apps) by November 2025 in favor of MCP servers. Migrate your extensions now!

What You Can Automate

Prerequisites

Before setting up GitHub MCP, you need:

1. Node.js (v18+)

node --version  # Should be v18.0.0 or higher

2. GitHub Personal Access Token

Creating a Classic Token:

1. Go to GitHub Settings → Developer settings → Personal access tokens → Tokens (classic)
2. Click “Generate new token (classic)”
3. Give it a descriptive name: MCP Server Access
4. Select scopes:

Recommended minimum scopes: repo, read:org

5. Click “Generate token”
6. Copy immediately - you won’t see it again!

Creating a Fine-Grained Token (More Secure):

1. Go to GitHub Settings → Developer settings → Personal access tokens → Fine-grained tokens
2. Click “Generate new token”
3. Set Resource owner (your account or org)
4. Set Repository access (All or Select repositories)
5. Select Permissions:
   • Repository permissions: Contents (Read/Write), Issues (Read/Write), Pull requests (Read/Write)
   • Account permissions: (optional based on needs)

3. MCP-Compatible Client

You need one of:

• Claude Desktop
• Cursor
• VS Code with GitHub Copilot (MCP GA as of July 2025)
• JetBrains IDEs (MCP allowlist controls available)
• Windsurf
• Cline
• Microsoft Copilot Studio (MCP support added March 2025)

For a comparison of AI coding tools, see the AI-Powered IDEs Comparison guide.

Installation & Configuration

Claude Desktop

Add to your claude_desktop_config.json:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json Windows: %APPDATA%/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "github": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "ghp_xxxxxxxxxxxx"
      }
    }
  }
}

Cursor

Add to your Cursor MCP settings or .cursor/mcp.json:

{
  "mcpServers": {
    "github": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "ghp_xxxxxxxxxxxx"
      }
    }
  }
}

GitHub Enterprise

For GitHub Enterprise, add the API URL:

{
  "mcpServers": {
    "github-enterprise": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "ghp_xxxxxxxxxxxx",
        "GITHUB_API_URL": "https://github.yourcompany.com/api/v3"
      }
    }
  }
}

Docker Installation

For isolated environments:

{
  "mcpServers": {
    "github": {
      "command": "docker",
      "args": [
        "run", "-i", "--rm",
        "-e", "GITHUB_PERSONAL_ACCESS_TOKEN=ghp_xxxxxxxxxxxx",
        "ghcr.io/modelcontextprotocol/server-github"
      ]
    }
  }
}

Verify Installation

After restarting your AI client, test with:

You: Search for the most starred TypeScript repositories on GitHub

Claude: I found these popular TypeScript repositories:
1. microsoft/TypeScript (95k+ stars) - The TypeScript language
2. denoland/deno (92k+ stars) - A JavaScript runtime
...

Available Tools

The GitHub MCP server provides 20+ tools. Here’s the complete reference:

Repository Management

Branch Management

Issue Management

Pull Request Management

Code Search

User Information

Practical Workflows

Workflow 1: Automated Issue Triage

Scenario: You receive bug reports and want AI to help organize them. For more on AI-assisted workflows, see the AI-Powered Workflows guide.

You: List all open issues in my-org/my-app that don't have labels

Claude: I found 12 unlabeled issues. Here are the first 5:
        - #156: App crashes on startup
        - #157: Button alignment issue
        - #158: Feature request: dark mode
        - #159: Performance slow on mobile
        - #160: Documentation outdated

You: Add appropriate labels to each one. Use 'bug', 'enhancement', 
     'documentation', or 'performance' based on the content.

Claude: I've labeled the issues:
        - #156: Added 'bug' label
        - #157: Added 'bug' label  
        - #158: Added 'enhancement' label
        - #159: Added 'performance' label
        - #160: Added 'documentation' label
        
        Would you like me to also add priority labels?

Workflow 2: Code Review Assistant

Scenario: Review a pull request and provide feedback.

You: Review the changes in PR #42 in my-org/my-app. 
     Focus on security and performance issues.

Claude: I've analyzed PR #42 "Add user authentication". Here's my review:

        **Security Issues (2 found):**
        1. Line 45: Password is logged to console (security risk)
           ```javascript
           console.log('Password:', password); // Remove this!

2. Line 78: SQL query uses string concatenation (SQL injection risk)

   const query = `SELECT * FROM users WHERE id = ${userId}`;
   // Should use parameterized query

Performance Issues (1 found):

1. Line 120: N+1 query inside a loop

Suggestions:

• Add rate limiting to login endpoint
• Use bcrypt for password hashing

Would you like me to add these as PR comments?

You: Yes, add comments for each issue

Claude: Done! I’ve added 4 comments to PR #42:

• Comment on line 45 about console.log
• Comment on line 78 about SQL injection
• Comment on line 120 about N+1 query
• General review comment with suggestions

### Workflow 3: New Project Setup

**Scenario**: Create a complete project structure with AI. For more on building AI applications, see the [Building Your First AI Application guide](/tech-articles/building-first-ai-application/).

```text
You: Create a new TypeScript project called "api-service" with:
     - README with project description
     - MIT license
     - Node .gitignore
     - Basic TypeScript config
     - Package.json with common scripts
     - src/index.ts with hello world

Claude: I'll create the repository and files:

        1. ✅ Created repository 'api-service'
        2. ✅ Added README.md with project description
        3. ✅ Added LICENSE (MIT)
        4. ✅ Added .gitignore for Node.js
        5. ✅ Added tsconfig.json
        6. ✅ Added package.json with scripts
        7. ✅ Added src/index.ts

        Repository URL: https://github.com/yourusername/api-service
        
        To get started:
        ```bash
        git clone https://github.com/yourusername/api-service
        cd api-service
        npm install
        npm run dev

### Workflow 4: Release Preparation

**Scenario**: Prepare for a release by reviewing recent changes.

```text
You: Summarize all merged PRs in my-org/my-app since version 2.0.0 
     and help me write release notes

Claude: I found 15 merged PRs since tag v2.0.0:

        **Features (6):**
        - #201: Add dark mode support
        - #205: Implement user preferences
        - #208: Add export to PDF
        - #212: New dashboard widgets
        - #215: API rate limiting
        - #218: Webhook notifications
        
        **Bug Fixes (7):**
        - #202: Fix login timeout
        - #206: Resolve memory leak
        ...
        
        **Documentation (2):**
        - #210: Update API docs
        - #216: Add migration guide
        
        Here's a draft for your release notes:
        
        ## Version 2.1.0 Release Notes
        
        ### 🚀 New Features
        - **Dark Mode**: Toggle between light and dark themes
        - **User Preferences**: Customize your experience
        ...
        
        Would you like me to create this as a GitHub release?

You: Yes, create the release as v2.1.0

Claude: Created release v2.1.0!
        URL: https://github.com/my-org/my-app/releases/tag/v2.1.0

Workflow 5: Cross-Repository Analysis

Scenario: Search for patterns across multiple repositories.

You: Find all repositories in my-org that use the deprecated 
     'request' npm package and haven't been updated in 6 months

Claude: I searched your organization and found 4 repositories 
        using the deprecated 'request' package:
        
        1. **my-org/legacy-api** (last updated: 8 months ago)
           - request@2.88.0 in package.json
           - 12 files importing request
           
        2. **my-org/old-webhook** (last updated: 14 months ago)
           - request@2.88.2 in package.json
           - 3 files importing request
           
        3. **my-org/data-sync** (last updated: 6 months ago)
           - request-promise@4.2.6 (depends on request)
           - 5 files using request-promise
           
        4. **my-org/integration-tests** (last updated: 10 months ago)
           - request@2.88.0 (dev dependency)
           - 8 test files using request
        
        Would you like me to create issues in each repo 
        to track the migration to 'node-fetch' or 'axios'?

Example Prompts

Repository Operations

# Search repositories
"Search GitHub for React component libraries with over 5000 stars"

"Find TypeScript projects related to AI that were updated in the last month"

# Create repository
"Create a new private repository called 'internal-tools' with a README"

"Create a public repo 'awesome-mcp' with description 'Curated list of MCP servers'"

# Fork repository
"Fork the vercel/next.js repository to my account"

# Get file contents
"Show me the package.json from facebook/react"

"Read the src/index.ts file from my-org/my-project on the develop branch"

Issue Management

# Create issues
"Create an issue in my-org/app titled 'Add dark mode support' with a detailed description of the feature request"

"Create a bug report in project-x for the login crash, include the error stack trace"

# List and filter issues
"Show all open bugs in my-org/app assigned to me"

"List issues in my-project labeled 'high-priority' that are unassigned"

"Find all issues in my-org mentioning 'performance' created this week"

# Update issues
"Close issue #42 with a comment explaining the fix"

"Add labels 'bug' and 'priority:high' to issue #50"

"Assign issue #55 to username 'johndoe'"

# Comment on issues
"Add a comment to issue #30 asking for reproduction steps"

"Comment on issue #35 that this is a duplicate of #20"

Pull Request Operations

# Create PRs
"Create a pull request from my feature/auth branch to main with the title 'Add authentication system'"

"Create a PR from develop to main titled 'Release v2.0' with a list of all changes"

# List and review PRs
"Show all PRs in my-org/app that need my review"

"What are the changes in PR #42?"

"Review PR #50 for code quality issues"

# Manage PRs
"Merge PR #42 using squash merge"

"Add @johndoe as a reviewer to PR #55"

"Close PR #60 with a comment explaining why it's being declined"

Code Search

# Search code
"Find all files in my-org that import 'moment' library"

"Search for uses of 'TODO' comments in my-project/src"

"Find all TypeScript files in my-org/app that export a function called 'formatDate'"

"Search for any hardcoded passwords in my-org (for security audit)"

Workflow Prompts

# Issue triage
"Go through all new issues in my-org/app from the last week and add appropriate labels"

# PR review
"Review the last 3 merged PRs in my-project and summarize the changes"

# Repository analysis
"Analyze my-org/app and identify potential security vulnerabilities in the dependencies"

# Documentation
"Read the source code of my-project and generate API documentation for the public functions"

# Release management
"List all commits since tag v1.0.0 and help me write changelog entries"

For tips on prompting AI effectively, see the Prompt Engineering Fundamentals guide.

Advanced Configuration

Multiple GitHub Accounts

Use different servers for work and personal GitHub:

{
  "mcpServers": {
    "github-work": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "ghp_work_token"
      }
    },
    "github-personal": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "ghp_personal_token"
      }
    }
  }
}

Combining with Git MCP

For complete version control integration, combine with Git MCP:

{
  "mcpServers": {
    "github": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "ghp_xxxx"
      }
    },
    "git": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-git", "--repository", "/path/to/repo"]
    }
  }
}

Now you can:

• Use GitHub MCP for remote operations (issues, PRs, repo management)
• Use Git MCP for local operations (status, diff, log, blame)

Combining with Filesystem MCP

For code analysis workflows:

{
  "mcpServers": {
    "github": { ... },
    "filesystem": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-filesystem", "/Users/me/projects"]
    }
  }
}

Workflow example:

You: Read the local changes in /projects/my-app/src/auth.ts, 
     then create a PR for them in my-org/my-app

Claude: I'll analyze your local changes and create a PR...
        [Reads local file]
        [Creates branch on GitHub]
        [Pushes changes]
        [Creates PR]
        Done! PR #72 created: https://github.com/my-org/my-app/pull/72

Rate Limits & Best Practices

GitHub API Rate Limits

Best Practices

Handling Rate Limits

If you hit rate limits:

You: I'm getting rate limit errors

Claude: GitHub API rate limit exceeded. Here's what you can do:
        1. Wait for the limit to reset (usually within the hour)
        2. Use more specific queries to reduce API calls
        3. Consider caching results for repeated lookups
        4. Check if you need all the data you're requesting

Troubleshooting

Issue: “Bad Credentials”

Symptoms: Server fails with authentication error

Solutions:

1. Check token hasn’t expired
2. Verify token is copied correctly (no extra spaces)
3. Ensure token has required scopes
4. Try regenerating the token

Issue: “Not Found”

Symptoms: Can’t access a repository

Solutions:

1. Verify repository name is correct (owner/repo)
2. Check if repo is private and token has repo scope
3. Confirm you have access to the repository
4. For org repos, ensure token has read:org scope

Issue: “Rate Limit Exceeded”

Symptoms: Operations fail with 403 error

Solutions:

1. Wait for rate limit reset (check headers)
2. Reduce number of operations
3. Use more specific queries
4. Consider upgrading to GitHub Pro for higher limits

Issue: “Server Not Connecting”

Symptoms: MCP server doesn’t appear in AI client

Solutions:

1. Validate JSON configuration syntax
2. Ensure Node.js is installed and in PATH
3. Restart the AI client completely
4. Check for error messages in client logs

Security Considerations

Token Security

For more on AI security best practices, see the Understanding AI Safety, Ethics, and Limitations guide.

Safe Operations

Audit Trail

GitHub maintains a complete audit trail of API actions. You can:

1. View Security Log in GitHub Settings
2. See all API-initiated actions
3. Identify and revoke problematic tokens

2025 Security Updates

⚠️ Security Best Practice: Always update to the latest MCP server version. The protocol now has enhanced protections against token theft and confused deputy attacks.

Related MCP Servers

Summary

The GitHub MCP Server is now the official standard for GitHub AI integrations:

• ✅ 20+ tools for complete GitHub coverage
• ✅ Natural language for all operations
• ✅ GitHub Copilot - MCP replaces deprecated Extensions (Nov 2025)
• ✅ VS Code GA - Native MCP support since July 2025
• ✅ Security-first with enhanced OAuth 2.0 and token binding
• ✅ Agentic AI Foundation - Now part of Linux Foundation governance

Common workflows enabled:

• Automated issue triage and labeling
• AI-assisted code review with Copilot
• One-command project setup
• Cross-repository analysis
• Release note generation

2025 Migration Note: If you’re using GitHub Copilot Extensions (GitHub Apps), migrate to MCP servers before November 2025.

Next: Learn about Playwright MCP Server → for browser automation with AI.

Questions about GitHub MCP? Check the official documentation or join the MCP Discord.