MCP GitHub Server Cannot Access Private Repositories (Cursor)

[attilapolgar]

Description

The @modelcontextprotocol/server-github package cannot access private GitHub repositories, consistently returning a "Not Found" error despite having a correctly authorized Personal Access Token (PAT). The same server successfully accesses public repositories with or without a token, indicating that the authentication mechanism is not being properly applied to API requests for private repositories.

Environment

• OS: macOS 24.3.0
• Node.js version: Latest stable
• MCP server package: @modelcontextprotocol/server-github (latest)
• Configuration: Using npx to run the server
• Cursor v0.46.8

Reproduction Steps

1. Create a GitHub Personal Access Token (PAT) with the repo scope
2. Configure the MCP server with this token:

   {
       "mcpServers": {
           "github": {
               "command": "npx",
               "args": [
                   "-y",
                   "@modelcontextprotocol/server-github"
               ],
               "env": {
                   "GITHUB_PERSONAL_ACCESS_TOKEN": "your_token_here"
               }
           }
       }
   }

3. Attempt to list issues from a private repository using:

   mcp__list_issues({owner: "OWNER", repo: "PRIVATE_REPO", per_page: 3})

Actual Result

{"error":"MCP error -32603: Not Found: Resource not found: Not Found"}

Expected Result

The MCP server should successfully list issues from the private repository, similar to how it works with public repositories.

Verification Steps

1. Token authentication works correctly with public repositories:

   mcp__list_issues({owner: "microsoft", repo: "vscode", per_page: 3})

   Result: Successfully returns issues from the microsoft/vscode repository.

2. Direct API calls to the private repository using the same token work properly:

   • Using curl:

     curl -H "Authorization: token GITHUB_TOKEN" https://api.github.com/repos/OWNER/PRIVATE_REPO/issues
     

     Result: Successfully returns issues from the private repository.

   • Using a custom Node.js script:

     // Custom script with same token
     const fetch = require('node-fetch');
     
     async function getIssues() {
       const response = await fetch(
         'https://api.github.com/repos/OWNER/PRIVATE_REPO/issues',
         {
           headers: {
             Authorization: `token ${process.env.GITHUB_TOKEN}`,
             'User-Agent': 'GitHub-API-Test'
           }
         }
       );
       
       if (response.ok) {
         const issues = await response.json();
         console.log(JSON.stringify(issues, null, 2));
       } else {
         console.error('Error:', response.status, await response.text());
       }
     }
     
     getIssues();

     Result: Successfully returns issues from the private repository.

Additional Information

• Various environment variable names were tried (GITHUB_TOKEN, GH_TOKEN) with no difference in results
• The token permissions were thoroughly verified and confirmed to have the necessary repo scope
• The error only occurs when trying to access private repositories through the MCP GitHub server
• The MCP server appears to be ignoring the authentication token when making API requests to GitHub for private repositories, as the behavior is identical with or without a token

[attilapolgar]

Potentially relevant issues or comments I discovered

#710 (comment)
#720
#677

[gthieleb]

Did you try with GITHUB_PERSONAL_ACCESS_TOKEN. Its stated in the README you need to scroll a bit down?

[jacobcolyvan]

Confirming same for me, I think its because the builds are failing which means the latest changes aren't being released to NPM.
I added a PR yesterday that should fix the typescript/NPM build – #722.

[attilapolgar]

Did you try with GITHUB_PERSONAL_ACCESS_TOKEN. Its stated in the README you need to scroll a bit down?

Thanks for the note @gthieleb , yes, that was my initial approach—I just didn’t include it in the example. I’ll update the issue accordingly.

[devucs]

I am still facing the same issue with a private repository, @attilapolgar did you be able to discover a fix?

[cliffhall]

Deprecation Notice: Development for server-github has been moved to GitHub in the http://github.com/github/github-mcp-server repo. PRs to server-github in this repo are no longer being merged.