Filesystem (Reference) vs GitHub MCP Server

A side-by-side comparison of two Files & Storage servers — tools, transport, auth, maintenance, and copy-paste config for each.

	Filesystem (Reference) Official MCP reference server for secure local filesystem read/write within allowed directories. Verified stdio (local) No auth TypeScript	GitHub MCP Server GitHub's official server for repos, issues, PRs, and Actions — local Docker or hosted remote. Verified stdio (local) API key Go
Category	Files & Storage	DevOps & Cloud
Language	TypeScript	Go
Transport	stdio (local)	stdio (local)
Auth	None	API key
GitHub stars	74k	31k
Last commit	5 months ago	5 days ago
Verified
Actively maintained
Install	`npx -y @modelcontextprotocol/server-filesystem /absolute/path/to/dir`	`docker run -i --rm -e GITHUB_PERSONAL_ACCESS_TOKEN ghcr.io/github/github-mcp-server`
Repo	Open	Open

Verdict

Pick Filesystem (Reference) if you prefer the more popular, battle-tested option, and you want zero-setup with no API key.

Pick GitHub MCP Server if you prefer its approach (github's official server for repos, issues, prs, and actions — local docker or hosted remote).

Add Filesystem (Reference)

Install / run

npx -y @modelcontextprotocol/server-filesystem /absolute/path/to/dir

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "filesystem-reference": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "/absolute/path/to/dir"
      ]
    }
  }
}

Add GitHub MCP Server

Install / run

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

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "github-mcp-server": {
      "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>"
      }
    }
  }
}

Requires Docker to be installed and running.

FAQ

Filesystem (Reference) or GitHub MCP Server — which is better?

Pick Filesystem (Reference) if you prefer the more popular, battle-tested option, and you want zero-setup with no API key. Pick GitHub MCP Server if you prefer its approach (github's official server for repos, issues, prs, and actions — local docker or hosted remote).

Can I use both Filesystem (Reference) and GitHub MCP Server?

Yes — MCP clients let you enable multiple servers at once. Add both configs to your client's mcpServers and use whichever tool fits the task.

Do Filesystem (Reference) and GitHub MCP Server work with Claude, Cursor and Windsurf?

Both do. Copy the per-client config below into Claude Desktop, Cursor, or Windsurf.

View Filesystem (Reference) →View GitHub MCP Server →More comparisons →