GitHub MCP Server Repository Not Found Error Troubleshooting Guide

Overview

Repository not found is a common repository access error for GitHub MCP servers [^1]. This usually indicates the repository doesn't exist, no access permission, or incorrect repository name format.

Error Symptoms

Repository not found
404 Not Found
MCP error -32603: failed to get pull request comments: 404 Not Found

Common Causes and Solutions

Cause 1: No Access to Private Repository

Solution: Ensure the token has permission to access private repositories [^2].

• Check token permissions in GitHub Settings > Developer settings > Personal access tokens
• Ensure repo permission is selected (access private repositories)
• Fine-grained Token needs explicit authorization for specific repositories

Cause 2: Incorrect Repository Name Format

Solution: Use correct repository name format owner/repo.

• Wrong: myrepo
• Correct: username/myrepo or org-name/repo-name

Cause 3: Repository Doesn't Exist or Deleted

Solution: Visit https://github.com/owner/repo in browser to confirm repository exists.

Cause 4: Insufficient Token Permissions

Solution: Check if token includes repo or read:org permissions.

Verify Repository Access

Test repository access using curl:

curl -H "Authorization: Bearer YOUR_TOKEN" \n  https://api.github.com/repos/owner/repo

Reference Sources

[^1]: GitHub Issue #727 - MCP GitHub Server cannot access private repositories
[^2]: GitHub Issue #735 - Private repository PR comments 404 error
[^3]: GitHub Docs - Token permissions - Official token permissions documentation