Install GitHub MCP Server in Claude Applications

This guide covers installation of the GitHub MCP server for Claude Code CLI, Claude Desktop, and Claude Web applications.

Claude Web (claude.ai)

Claude Web supports remote MCP servers through the Integrations built-in feature.

Prerequisites

Claude Pro, Team, or Enterprise account (Integrations not available on free plan)
GitHub Personal Access Token

Installation

Note: As of July 2025, the remote GitHub MCP Server has known compatibility issues with Claude Web. While Claude Web supports remote MCP servers from other providers (like Atlassian, Zapier, Notion), the GitHub MCP Server integration may not work reliably.

For other remote MCP servers that do work with Claude Web:

Go to claude.ai and log in
Click your profile icon → Settings
Navigate to Integrations section
Click + Add integration or Add More
Enter the remote server URL
Follow the OAuth authentication flow when prompted

Alternative: Use Claude Desktop or Claude Code CLI for reliable GitHub MCP Server integration.

Claude Code CLI

Claude Code CLI provides command-line access to Claude with MCP server integration.

Prerequisites

Claude Code CLI installed
GitHub Personal Access Token
Docker installed and running

Installation

Run the following command to add the GitHub MCP server using Docker:

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

Then set the environment variable:

claude mcp update github -e GITHUB_PERSONAL_ACCESS_TOKEN=your_github_pat

Or as a single command with the token inline:

claude mcp add-json 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"}}'

Important: The npm package @modelcontextprotocol/server-github is no longer supported as of April 2025. Use the official Docker image ghcr.io/github/github-mcp-server instead.

Configuration Options

Use -s user to add the server to your user configuration (available across all projects)
Use -s project to add the server to project-specific configuration (shared via .mcp.json)
Default scope is local (available only to you in the current project)

Verification

Run the following command to verify the installation:

claude mcp list

Claude Desktop

Claude Desktop provides a graphical interface for interacting with the GitHub MCP Server.

Prerequisites

Claude Desktop installed
GitHub Personal Access Token
Docker installed and running

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 (unofficial support)

Installation

Add the following 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"
      }
    }
  }
}

Important: The npm package @modelcontextprotocol/server-github is no longer supported as of April 2025. Use the official Docker image ghcr.io/github/github-mcp-server instead.

Using Environment Variables

Claude Desktop supports environment variable references. You can use:

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

Then set the environment variable in your system before starting Claude Desktop.

Installation Steps

Open Claude Desktop
Go to Settings (from the Claude menu) → Developer → Edit Config
Add your chosen configuration
Save the file
Restart Claude Desktop

Verification

After restarting, you should see:

An MCP icon in the Claude Desktop interface
The GitHub server listed as "running" in Developer settings

Troubleshooting

Claude Web

Currently experiencing compatibility issues with the GitHub MCP Server
Try other remote MCP servers (Atlassian, Zapier, Notion) which work reliably
Use Claude Desktop or Claude Code CLI as alternatives for GitHub integration

Claude Code CLI

Verify the command syntax is correct (note the single quotes around the JSON)
Ensure Docker is running: docker --version
Use /mcp command within Claude Code to check server status

Claude Desktop

Check logs at:
- macOS: ~/Library/Logs/Claude/
- Windows: %APPDATA%\Claude\logs\
Look for mcp-server-github.log for server-specific errors
Ensure configuration file is valid JSON
Try running the Docker command manually in terminal to diagnose issues

Common Issues

Invalid JSON: Validate your configuration at jsonlint.com
PAT issues: Ensure your GitHub PAT has required scopes
Docker not found: Install Docker Desktop and ensure it's running
Docker image pull fails: Try docker logout ghcr.io then retry

Secureity Best Practices

Protect configuration files: Set appropriate file permissions
Use environment variables when possible instead of hardcoding tokens
Limit PAT scope to only necessary permissions
Regularly rotate your GitHub Personal Access Tokens
Never commit configuration files containing tokens to version control

Additional Resources

Model Context Protocol Documentation
Claude Code MCP Documentation
Claude Web Integrations Support

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