GitHub MCP Setup

Guide users through configuring their GitHub Personal Access Token (PAT) for the GitHub MCP server integration.

When to Activate

• User wants to set up GitHub MCP integration
• User mentions GitHub token configuration
• User asks about GitHub authentication for Claude Code
• GitHub MCP server fails due to missing token

Overview

The GitHub MCP server provides repository management, file operations, issue tracking, and PR functionality directly within Claude Code. It requires a GitHub Personal Access Token (PAT) for authentication.

Setup Process

Step 1: Check Current Token Status

First, check if the token is already configured:

# Check if GITHUB_PERSONAL_ACCESS_TOKEN is set
if [ -n "$GITHUB_PERSONAL_ACCESS_TOKEN" ]; then
  echo "GitHub token is configured (length: ${#GITHUB_PERSONAL_ACCESS_TOKEN} chars)"
else
  echo "GitHub token is NOT configured"
fi

Step 2: Create a GitHub Personal Access Token

If no token exists, guide the user:

1. Navigate to GitHub Token Settings:

   • Go to: https://github.com/settings/tokens?type=beta
   • Or: GitHub Settings > Developer settings > Personal access tokens > Fine-grained tokens

2. Create New Token:

   • Click "Generate new token"
   • Give it a descriptive name (e.g., "Claude Code MCP")
   • Set expiration (recommend 90 days or custom)
   • Select repository access (recommend "All repositories" or specific repos)

3. Required Permissions (minimum for full functionality):

   • Repository permissions:
     • Contents: Read and write
     • Issues: Read and write
     • Pull requests: Read and write
     • Metadata: Read-only (automatically selected)
   • Account permissions (optional):
     • Email addresses: Read-only

4. Generate and Copy Token:

   • Click "Generate token"
   • Copy the token immediately (it won't be shown again)

Step 3: Configure Environment Variable

Add the token to your shell profile for persistence:

For Zsh (default on macOS):

echo 'export GITHUB_PERSONAL_ACCESS_TOKEN="ghp_your_token_here"' >> ~/.zshrc
source ~/.zshrc

For Bash:

echo 'export GITHUB_PERSONAL_ACCESS_TOKEN="ghp_your_token_here"' >> ~/.bashrc
source ~/.bashrc

For Fish:

set -Ux GITHUB_PERSONAL_ACCESS_TOKEN "ghp_your_token_here"

Step 4: Verify Configuration

After setting the token, restart Claude Code and verify:

# Verify token is set
echo "Token configured: $([ -n \"$GITHUB_PERSONAL_ACCESS_TOKEN\" ] && echo 'Yes' || echo 'No')"

Then run /mcp in Claude Code to see the GitHub MCP server listed.

Troubleshooting

Token Not Found

If the GitHub MCP server reports a missing token:

1. Verify the environment variable is set:

   echo $GITHUB_PERSONAL_ACCESS_TOKEN
   

2. If empty, check your shell profile contains the export

3. Source your profile or restart the terminal:

   source ~/.zshrc  # or ~/.bashrc
   

4. Restart Claude Code to pick up the new environment

Token Invalid or Expired

If you get authentication errors:

1. Check token expiration at https://github.com/settings/tokens
2. Generate a new token if expired
3. Update your shell profile with the new token
4. Restart Claude Code

Insufficient Permissions

If certain operations fail:

1. Review token permissions at https://github.com/settings/tokens
2. Edit the token to add required permissions
3. Note: Some actions require specific scopes (e.g., workflow for GitHub Actions)

Security Best Practices

1. Never commit tokens: Add your shell profile to .gitignore
2. Use fine-grained tokens: Prefer fine-grained over classic tokens for better security
3. Limit scope: Only grant permissions you actually need
4. Set expiration: Use short-lived tokens when possible
5. Rotate regularly: Regenerate tokens periodically
6. Use secrets managers: Consider 1Password, Keychain, or similar for token storage

Available GitHub MCP Tools

Once configured, you'll have access to:

• Repository Management: Create, fork, search repositories
• File Operations: Read, create, update files and directories
• Issue Tracking: Create, update, search, comment on issues
• Pull Requests: Create PRs, add reviewers, merge
• Branch Management: Create, list, delete branches
• Search: Search code, issues, PRs, users across GitHub

Quick Reference

Item	Value
Environment Variable	GITHUB_PERSONAL_ACCESS_TOKEN
Token Settings URL	https://github.com/settings/tokens
Token Type	Fine-grained (recommended) or Classic
MCP Server	Hosted at api.githubcopilot.com/mcp

Next Steps

After successful setup:

1. Run /mcp to verify the GitHub server is connected
2. Try a simple command like "list my GitHub repositories"
3. Explore available tools with "what GitHub tools are available?"