Install GitHub MCP Server in Claude Applications

Claude Code CLI

Prerequisites

• Claude Code CLI installed
• GitHub Personal Access Token
• For local setup: Docker installed and running
• Open Claude Code inside the directory for your project (recommended for best experience and clear scope of configuration)

For security, avoid hardcoding your token. One common approach:

1. Store your token in .env file

GITHUB_PAT=your_token_here

2. Add to .gitignore

echo -e ".env\n.mcp.json" >> .gitignore

Remote Server Setup (Streamable HTTP)

Note: For Claude Code versions 2.1.1 and newer, use the add-json command format below. For older versions, see the legacy command format.

Windows / CLI note: claude mcp add-json may return Invalid input when adding an HTTP server. If that happens, use the legacy claude mcp add --transport http ... command format below.

1. Run the following command in the terminal (not in Claude Code CLI):

claude mcp add-json github '{"type":"http","url":"https://api.githubcopilot.com/mcp","headers":{"Authorization":"Bearer YOUR_GITHUB_PAT"}}'

With an environment variable:

claude mcp add-json github '{"type":"http","url":"https://api.githubcopilot.com/mcp","headers":{"Authorization":"Bearer '"$(grep GITHUB_PAT .env | cut -d '=' -f2)"'"}}'

About the --scope flag (optional): Use this to specify where the configuration is stored:

• local (default): Available only to you in the current project (was called project in older versions)
• project: Shared with everyone in the project via .mcp.json file
• user: Available to you across all projects (was called global in older versions)

Example: Add --scope user to the end of the command to make it available across all projects.

2. Restart Claude Code
3. Run claude mcp list to see if the GitHub server is configured

Local Server Setup (Docker required)

With Docker

1. Run the following command in the terminal (not in Claude Code CLI):

claude mcp add github -e GITHUB_PERSONAL_ACCESS_TOKEN=YOUR_GITHUB_PAT -- docker run -i --rm -e GITHUB_PERSONAL_ACCESS_TOKEN ghcr.io/github/github-mcp-server

With an environment variable:

claude mcp add github -e GITHUB_PERSONAL_ACCESS_TOKEN=$(grep GITHUB_PAT .env | cut -d '=' -f2) -- docker run -i --rm -e GITHUB_PERSONAL_ACCESS_TOKEN ghcr.io/github/github-mcp-server

2. Restart Claude Code
3. Run claude mcp list to see if the GitHub server is configured

With a Binary (no Docker)

1. Download release binary
2. Add to your PATH
3. Run:

claude mcp add-json github '{"command": "github-mcp-server", "args": ["stdio"], "env": {"GITHUB_PERSONAL_ACCESS_TOKEN": "YOUR_GITHUB_PAT"}}'

2. Restart Claude Code
3. Run claude mcp list to see if the GitHub server is configured

Verification

claude mcp list
claude mcp get github

For Older Versions of Claude Code

If you're using Claude Code version 2.1.0 or earlier, use this legacy command format:

claude mcp add --transport http github https://api.githubcopilot.com/mcp -H "Authorization: Bearer YOUR_GITHUB_PAT"

With an environment variable:

claude mcp add --transport http github https://api.githubcopilot.com/mcp -H "Authorization: Bearer $(grep GITHUB_PAT .env | cut -d '=' -f2)"

Windows (PowerShell)

If you see missing required argument 'name', put the server name immediately after claude mcp add:

$pat = "YOUR_GITHUB_PAT"
claude mcp add github --transport http https://api.githubcopilot.com/mcp/ -H "Authorization: Bearer $pat"

Claude Desktop

⚠️ Note: Some users have reported compatibility issues with Claude Desktop and Docker-based MCP servers. We're investigating. If you experience issues, try using another MCP host, while we look into it!

Prerequisites

• Claude Desktop installed (latest version)
• GitHub Personal Access Token
• Docker installed and running

Note: Claude Desktop supports MCP servers that are both local (stdio) and remote ("connectors"). Remote servers can generally be added via Settings → Connectors → "Add custom connector". However, the GitHub remote MCP server requires OAuth authentication through a registered GitHub App (or OAuth App), which is not currently supported. Use the local Docker setup instead.

Configuration File Location

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%\Claude\claude_desktop_config.json
• Linux: ~/.config/Claude/claude_desktop_config.json

Local Server Setup (Docker)

Add this codeblock to your claude_desktop_config.json:

{
  "mcpServers": {
    "github": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "-e",
        "GITHUB_PERSONAL_ACCESS_TOKEN",
        "ghcr.io/github/github-mcp-server"
      ],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "YOUR_GITHUB_PAT"
      }
    }
  }
}

Manual Setup Steps

1. Open Claude Desktop
2. Go to Settings → Developer → Edit Config
3. Paste the code block above in your configuration file
4. If you're navigating to the configuration file outside of the app:
   • macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
   • Windows: %APPDATA%\Claude\claude_desktop_config.json
5. Open the file in a text editor
6. Paste one of the code blocks above, based on your chosen configuration (remote or local)
7. Replace YOUR_GITHUB_PAT with your actual token or $GITHUB_PAT environment variable
8. Save the file
9. Restart Claude Desktop

Troubleshooting

Authentication Failed:

• Verify PAT has repo scope
• Check token hasn't expired

Remote Server:

• Verify URL: https://api.githubcopilot.com/mcp

Docker Issues (Local Only):

• Ensure Docker Desktop is running
• Try: docker pull ghcr.io/github/github-mcp-server
• If pull fails: docker logout ghcr.io then retry

Server Not Starting / Tools Not Showing:

• Run claude mcp list to view currently configured MCP servers
• Validate JSON syntax
• If using an environment variable to store your PAT, make sure you're properly sourcing your PAT using the environment variable
• Restart Claude Code and check /mcp command
• Delete the GitHub server by running claude mcp remove github and repeating the setup process with a different method
• Make sure you're running Claude Code within the project you're currently working on to ensure the MCP configuration is properly scoped to your project
• Check logs:
  • Claude Code: Use /mcp command
  • Claude Desktop: ls ~/Library/Logs/Claude/ and cat ~/Library/Logs/Claude/mcp-server-*.log (macOS) or %APPDATA%\Claude\logs\ (Windows)

Important Notes

• The npm package @modelcontextprotocol/server-github is deprecated as of April 2025
• Remote server requires Streamable HTTP support (check your Claude version)
• For Claude Code configuration scopes, see the --scope flag documentation in the Remote Server Setup section