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Setting up GitHub MCP Server: Where To Find Your Personal Access Token

April 29, 2025•Andrew Huang

Setting up a GitHub MCP Server can be a game-changer, unlocking new levels of collaboration and efficiency in your projects. But before you can start leveraging its full potential, there's an essential step you can’t overlook: finding your Personal Access Token.

Understanding Personal Access Tokens

Personal Access Tokens (PATs) provide a more secure way to authenticate and interact with GitHub than passwords. They let you control access levels and manage permissions flexibly, crucial for systems like MCP Servers that need consistent API communication.

Why You Need a Personal Access Token for MCP Server

The MCP Server uses your PAT to securely interact with GitHub—handling tasks like managing webhooks or repositories without exposing sensitive credentials. It’s an easy-to-use, OAuth-free way to keep things running securely.

Step-by-Step Guide to Generating a PAT

  1. Log into GitHub: Make sure you have access to generate a PAT.
  2. Navigate to Settings: Click your profile picture → Settings.
  3. Access Developer Settings: Scroll down in the sidebar and open “Developer settings.”
  4. Generate New Token: Click “Generate new token” under Personal Access Tokens.
  5. Select Scopes: Typically, repo and admin:repo_hook are needed.
  6. Generate Token: GitHub will show the token once. Copy and store it securely.

Locating and Managing Your PAT

Go to Settings → Developer settings → Personal access tokens to see and manage existing tokens. You won’t see the token string again, so keep it stored safely!

Best Practices for PAT Security

  • Use Least Privilege: Only grant what’s needed.
  • Store Securely: Use a password manager or environment variable.
  • Rotate Regularly: Avoid long-term exposure.
  • Audit Access: Revoke unused tokens.
  • Monitor Usage: Use GitHub’s logs to watch for suspicious activity.

Common Setup Issues (and Fixes)

  • Invalid Token: Copy carefully or regenerate.
  • Insufficient Permissions: Adjust scopes to what’s actually needed.
  • Expired Token: Generate a fresh one and update your config.
  • Network Issues: Check API access and proxy/firewall configs.
  • Rate Limiting: Implement retries/backoffs on API calls.

Securing Your MCP Server

  • Use Environment Variables: Avoid hardcoding secrets.
  • Implement Access Controls: RBAC and secure storage.
  • Encrypt Tokens: Consider using a secrets manager.
  • Conduct Audits: Stay ahead of potential issues.
  • Stay Updated: Patch your server regularly.

Alternatives to PATs

  • OAuth Apps: Great for user-based permission flows.
  • SSH Keys: Ideal for repo-level command-line tasks.
  • GitHub Apps: More scalable, secure, and structured than PATs.
  • API Tokens: Specific to things like GitHub Actions.

Conclusion and Next Steps

Mastering Personal Access Tokens gives you a clean, secure way to integrate GitHub with your MCP Server. By following best practices and knowing your options, you can keep your environment tight and efficient. Now go secure that server and build with confidence.