Connect GitHub

GitHub’s remote MCP server requires a Personal Access Token rather than OAuth — it doesn’t support Dynamic Client Registration, so the one-click OAuth flow isn’t available for third-party gateways. You generate a token with the right scopes for the toolsets you need, choose a toolset URL, and add the server with an Authorization header.

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What you need

Bring the following before you open MCP Manager:

• A GitHub account with access to the repositories and resources your team’s AI tools will need to reach.
• The ability to create a Personal Access Token (PAT) on that account — either a fine-grained PAT scoped to specific repositories, or a classic PAT with the right scopes. Fine-grained PATs are recommended; they give you tighter control over which repositories the token can reach. Note that some organizations require admin approval before a fine-grained PAT can be used — see Gotchas if you’re working inside a GitHub organization.
• The right scopes for the toolsets you plan to use. See Scopes by toolset below.
• Optionally, a GitHub organization with a Copilot Business or Enterprise plan if you want access to security toolsets. Some tools require it.

The connection uses a shared token, not per-user OAuth. Every user on the gateway acts as the GitHub identity that owns the PAT. Read Identity and attribution before connecting if per-user accountability matters to your deployment.

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Scopes by toolset

GitHub’s MCP server is organized into toolsets. The scopes your PAT needs depend on which ones you enable. Each toolset also has its own URL path — more on that in Connect the server. Start with the default toolsets (repos, issues, pull_requests, context) and the repo scope. Add further scopes only when you add a toolset that needs them — over-provisioned PATs are the leading cause of unintended access.

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Connect the server

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Identity and attribution

GitHub’s remote MCP server does not support per-user OAuth for third-party clients, so this connection uses a shared token — every user on the gateway acts as the GitHub account that owns the PAT. All tool calls appear in GitHub’s own logs as that account, not as the individual team member who triggered them. MCP Manager’s own logs do attribute calls to the real user, so you retain per-person visibility within MCP Manager. But any GitHub-side audit trail — API usage logs, repository event logs — will reflect the PAT owner. Two patterns that follow from this:

• Read/write split. Add the server twice: once with a read-only toolset URL (append /readonly) using a scoped service-account PAT for broad access, and again with the write-capable URL requiring each user to supply their own PAT. That way reads are frictionless and shared, while writes carry the individual’s token — and therefore their identity in GitHub’s logs. See Adding the same server more than once.
• Use a dedicated account token. Rather than a personal token that expires when someone leaves, create a dedicated GitHub machine account or use a GitHub App installation token for the credential. The connection then survives team turnover.

See per-user versus shared identity for how this maps to gateway identity schemes.

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Gotchas & things to keep in mind

OAuth will not work. GitHub’s remote MCP server does not support Dynamic Client Registration (DCR), which is what MCP Manager uses to self-register for the standard OAuth flow. If you paste the base URL and expect an OAuth prompt, you won’t get one — you must supply the Authorization: Bearer <PAT> header manually. This is a GitHub-side constraint. That said, per-user identity is still achievable: configure the server assignment as per-user in the gateway, and each teammate will be prompted to enter their own PAT on first connection. See Identity Controls. Fine-grained PATs cannot grant workflow scope. If you need the Actions toolset (https://api.githubcopilot.com/mcp/x/actions), you must use a classic PAT and check the workflow scope. Fine-grained PATs do not include it. PAT expiry breaks the connection. When a token expires, tool calls start returning 401 errors. Fine-grained PATs allow a “No expiration” option unless your organization enforces a maximum lifetime policy; classic PATs can also be set to never expire. If you do set an expiration, put a reminder in place to rotate the token and update the header value in MCP Manager before it hits. Organization PAT policies may block fine-grained tokens. Some GitHub organizations restrict which PAT types can be used, or require admin approval for fine-grained PATs. If your token is rejected, check your organization’s Personal access token policies under GitHub Organization Settings. Enterprise Server is not supported. GitHub’s remote MCP server at api.githubcopilot.com is not available for GitHub Enterprise Server (self-hosted). GHES customers must run the local Docker-based server (ghcr.io/github/github-mcp-server) instead — that is a different setup not covered here. GitHub Enterprise Cloud with data residency uses a different base URL. Replace api.githubcopilot.com with copilot-api.<your-subdomain>.ghe.com — for example, if your instance is octocorp.ghe.com, the MCP server URL is https://copilot-api.octocorp.ghe.com/mcp. Security toolsets require paid licenses. The code_security, dependabot, and secret_protection toolsets require GitHub Advanced Security or GitHub Secret Protection to be enabled on the repositories in question. The tools will appear in the gateway but return errors on repositories where the feature isn’t licensed. Experiments toolset is unstable. The experiments toolset (https://api.githubcopilot.com/mcp/x/experiments) exposes features GitHub has not declared stable. Tool names, behavior, and availability may change without notice.

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Further reading

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External sources