How to Set Up the GitHub MCP Server for Repository Management

Set Up the GitHub MCP Server

The GitHub MCP server provides comprehensive access to GitHub's REST API. It transforms your AI agent into an automated project manager and code reviewer capable of managing repositories, triaging issues, and drafting pull requests.

Prerequisites

• ▸A GitHub account.
• ▸A GitHub Personal Access Token (PAT).
• ▸Node.js 18+ installed locally.

Creating a Fine-Grained Personal Access Token

It is strongly recommended to use Fine-Grained Tokens rather than Classic Tokens for security.

1. ▸Go to GitHub Settings → Developer Settings → Personal Access Tokens → Fine-grained tokens.
2. ▸Click Generate new token.
3. ▸Set the Repository access to "Only select repositories".
4. ▸Assign the following Permissions:
   • ▸Contents (Read/Write)
   • ▸Issues (Read/Write)
   • ▸Pull Requests (Read/Write)
5. ▸Generate the token and copy it immediately.

Configuration Setup

Add the following to your MCP client config:

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

Available Tools

The GitHub server exposes a massive suite of tools to the agent:

Repository Operations

• ▸create_repository / search_repositories / get_file_contents / push_files / create_branch

Issue Management

• ▸create_issue / list_issues / update_issue / add_issue_comment

Pull Request Operations

• ▸create_pull_request / list_pull_requests / merge_pull_request / get_pull_request_diff

Example Workflows

• ▸Code Review Assistant: "Review the latest pull request on my-org/my-repo, look for security vulnerabilities, and add a comment on the issue with your findings."
• ▸Issue Triage: "List all open issues labeled 'bug' in my-repo and categorize them by severity based on the user descriptions."
• ▸Repository Analysis: "Analyze the codebase structure of my-org/my-repo and create a README.md outline."

Troubleshooting

• ▸403 Forbidden / SAML SSO: If your organization enforces SAML Single Sign-On, your PAT will be rejected by the API unless you explicitly authorize the token for use with that specific organization in the GitHub UI.
• ▸404 Not Found: This almost always means your token lacks the correct permissions to view the repository, or the repository name is misspelled. Remember that repos must be prefixed with their owner (owner-name/repo-name).
• ▸Token Expiry: Fine-grained tokens have a maximum lifespan of 1 year. If your agent suddenly loses access, verify your PAT hasn't expired.

Using with OpenAI Codex

You can use this MCP server with the OpenAI Codex CLI by adding it to your configuration:

codex mcp add --name github --command "npx -y @modelcontextprotocol/server-github" --env GITHUB_PERSONAL_ACCESS_TOKEN=ghp_your_token

For a full list of recommended servers, see Best MCP Servers for OpenAI Codex.