How to Configure MCP Server to Connect to GitHub Enterprise Cloud

Configure the GitHub MCP Server to connect to GitHub Enterprise Cloud by setting the Host field in MCPServerConfig to your ghe.com subdomain using either the GITHUB_HOST environment variable, the --gh-host command-line flag, or the X-MCP-Host HTTP header.

The GitHub MCP Server enables AI assistants to interact with GitHub repositories through the Model Context Protocol (MCP). When you need to configure the MCP server to connect to GitHub Enterprise Cloud—particularly for data-residency deployments using the ghe.com domain—you must explicitly specify the host endpoint so the server routes API requests correctly.

Understanding the Host Configuration Architecture

The MCPServerConfig.Host Field

In pkg/github/server.go, the server defines a configuration struct that controls all GitHub API interactions:

type MCPServerConfig struct {
    Host  string
    Token string
    // ... other fields
}

The Host field determines whether the server connects to github.com or your private GitHub Enterprise Cloud instance. When left empty, the server defaults to the public GitHub.com API endpoints.

How the Server Builds API Clients

The pkg/github/dependencies.go file (lines 82-90) handles the construction of REST, GraphQL, and raw HTTP clients using your configured host. The server calls githubv4.NewEnterpriseClient unconditionally, passing the parsed host value to ensure all subsequent API calls—whether for issues, pull requests, or repository data—target your Enterprise Cloud installation.

Three Methods to Configure GitHub Enterprise Cloud Connection

Environment Variable GITHUB_HOST (STDIO Mode)

For local STDIO-based MCP servers, set the GITHUB_HOST environment variable before launching the server. This method is documented in README.md under the section "GitHub Enterprise Server and Enterprise Cloud with data residency (ghe.com)" and in .github/copilot-instructions.md.

The server reads this variable at startup and assigns it to MCPServerConfig.Host.

Command-Line Flag --gh-host

When running the server binary directly, use the --gh-host flag to specify your Enterprise Cloud domain:

go run ./cmd/github-mcp-server stdio \
  --gh-host https://mycompany.ghe.com \
  --token $GITHUB_PAT

This flag is parsed by the CLI and passed directly to the configuration struct in pkg/github/server.go.

HTTP Header X-MCP-Host (Remote Mode)

For remote HTTP deployments where the MCP server runs as a service, you can override the host per-request using the X-MCP-Host header. This is handled in pkg/http/middleware/request_config.go, which applies request-level configuration overrides.

This approach allows a single MCP server instance to serve multiple GitHub Enterprise Cloud organizations by routing requests based on the header value.

Configuration Examples for GitHub Enterprise Cloud

Local STDIO Server with Environment Variable

Configure your MCP client (such as Claude Desktop or Copilot) to pass the host via environment variables:

{
  "type": "stdio",
  "command": "go",
  "args": [
    "run",
    "./cmd/github-mcp-server",
    "stdio",
    "--toolsets=issues,pull_requests"
  ],
  "env": {
    "GITHUB_PERSONAL_ACCESS_TOKEN": "ghp_your_token_here",
    "GITHUB_HOST": "https://mycompany.ghe.com"
  }
}

Local STDIO Server with CLI Flag

Alternatively, pass the host directly as a command-line argument:

go run ./cmd/github-mcp-server stdio \
  --gh-host https://mycompany.ghe.com \
  --toolsets=issues,pull_requests \
  --token $GITHUB_PAT

Remote HTTP Server with Per-Request Headers

For HTTP-based MCP servers, configure your client to send the host header:

{
  "type": "http",
  "url": "https://api.githubcopilot.com/mcp/",
  "headers": {
    "X-MCP-Host": "https://mycompany.ghe.com",
    "X-MCP-Toolsets": "issues,repo",
    "Authorization": "Bearer $COPILOT_TOKEN"
  }
}

Docker Deployment with Environment Variable

When running the official container image, pass the host as an environment variable:

export GITHUB_HOST=https://mycompany.ghe.com
export GITHUB_PERSONAL_ACCESS_TOKEN=ghp_your_token_here

docker run -e GITHUB_HOST -e GITHUB_PERSONAL_ACCESS_TOKEN ghcr.io/github/github-mcp-server

Summary

• The GitHub MCP Server uses MCPServerConfig.Host in pkg/github/server.go to determine which GitHub instance to target.
• You can configure GitHub Enterprise Cloud connectivity through three methods: the GITHUB_HOST environment variable, the --gh-host command-line flag, or the X-MCP-Host HTTP header for remote deployments.
• The host value must include the https:// scheme and follow the format https://YOURSUBDOMAIN.ghe.com for data-residency Enterprise Cloud instances.
• All API clients (REST, GraphQL, and raw HTTP) are constructed in pkg/github/dependencies.go using the configured host, ensuring consistent routing for all tool operations.

Frequently Asked Questions

What URL format should I use for GitHub Enterprise Cloud?

You must include the full URL scheme and subdomain. For GitHub Enterprise Cloud with data residency, use https://YOURSUBDOMAIN.ghe.com. Omitting the https:// prefix causes the server to default to http://, which GitHub Enterprise Cloud does not accept.

Can I switch between GitHub.com and Enterprise Cloud dynamically?

Yes, but the method depends on your deployment mode. For local STDIO servers, you must restart the server with a different GITHUB_HOST value or --gh-host flag. For remote HTTP servers, you can switch dynamically by sending different X-MCP-Host header values per request, as handled by pkg/http/middleware/request_config.go.

Where is the host configuration stored internally?

The host value is stored in the Host field of the MCPServerConfig struct defined in pkg/github/server.go. This configuration object is passed to github.NewMCPServer and subsequently used by pkg/github/dependencies.go to instantiate API clients. The value is also logged at server startup for verification.

Do I need different authentication for Enterprise Cloud?

No, the authentication mechanism remains the same. You still use a GitHub Personal Access Token (PAT) passed via the GITHUB_PERSONAL_ACCESS_TOKEN environment variable or --token flag. However, ensure your token has the appropriate scopes for your Enterprise Cloud organization and that the token was generated on the specific Enterprise Cloud instance you are targeting.

{
  "mcpServers": {
    "instagit": {
      "command": "npx",
      "args": ["-y", "instagit@latest"]
    }
  }
}