Unable to connect Gemini CLI to MCP Server

[SirHawbly]

Describe the bug

Sabre is trying to setup MCP in Gemini CLI, but their outgoing requests keep getting a "missing header" response, though it sounds like things are working in their JetBrains client. They seem to be using the steps on this page and the configs in this section here. Has anyone seen this before?

Links:

• Ticket: https://github.zendesk.com/agent/tickets/3760913

• MCP slack: https://github.slack.com/archives/C08GU0TBFGR/p1760118858005809

• copilot slack: https://github.slack.com/archives/C04FG033SGJ/p1760119006551659

Customer emails:

Post 1

Regardless the configuration below the GitHub MCP status is always returning message as below.
Assume that it explains why Gemini CLI is not able to connect to it - what can be a cause of it?

$ curl https://api.githubcopilot.com/mcp/ping -H "Authorization: github_pat_XXX"
GET requests are disabled

https://github.com/github/github-mcp-server/blob/main/docs/installation-guides/install-gemini-cli.md

Post 2

The message below is not changing regardless the settings to be or not active:

Post 3

I found the time to debug it one more time: I have MCP enabled, I can use those in IDE (copilot plugin) but not in gemini cli.

MCP active on the Org level:

MCP works in IDE:

{
  "servers": {
    "github": {
      "url": "https://api.githubcopilot.com/mcp/",
      "requestInit": {
        "headers": {
          "Authorization": "Bearer ghp_XXX"
        }
      }
    }
  }
}

MCP does not work in Gemini CLI:

{
  "mcpServers": {
    "github": {
      "httpUrl": "https://api.githubcopilot.com/mcp/",
      "trust": true,
      "headers": {
        "Authorization": "Bearer ghp_XXX"
      }
    }
  }
}

Gemini config files taken from: https://github.com/github/github-mcp-server/blob/main/docs/installation-guides/install-gemini-cli.md

The MCP API response seems to be irrelevant since always the same:

$ curl https://api.githubcopilot.com/mcp/ping -H "Authorization: ${GITHUB_TOKEN}"
GET requests are disabled

Post 4

This is exactly the config I'm using, if the suggestion was that I accidently used Copilot specific settings (for such config the list of MCP server is empty). I see in debug mode that it is not sending the auth header, in contrast to what is defined in the config.

Post 5

Any hints to what the permissions the token should have... I have tried user, org level tokens and it is always the same 404 (and obviously 401 if the token is not there).

curl -I https://api.githubcopilot.com/mcp/_ping -H "Authorization: ${GITHUB_TOKEN}"
HTTP/2 404 
access-control-allow-headers: Content-Type, Authorization, X-MCP-Readonly, X-MCP-Toolsets, Mcp-Session-Id
access-control-allow-methods: GET, POST, OPTIONS
access-control-allow-origin: *
access-control-max-age: 86400
content-length: 19
content-security-policy: default-src 'none'; sandbox
content-type: text/plain; charset=utf-8
date: Tue, 07 Oct 2025 20:01:48 GMT
server: github-mcp-server-remote
strict-transport-security: max-age=31536000
x-content-type-options: nosniff
x-github-backend: Kubernetes
x-github-request-id: A002:B8102:2BF320:33EA37:68E571AC

curl -I https://api.githubcopilot.com/mcp/_ping
 curl -I https://api.githubcopilot.com/mcp/_ping
HTTP/2 401 
content-security-policy: default-src 'none'; sandbox
content-type: text/plain; charset=utf-8
strict-transport-security: max-age=31536000
www-authenticate: Bearer error="invalid_request", error_description="No access token was provided in this request", resource_metadata="https://api.githubcopilot.com/.well-known/oauth-protected-resource/mcp/_ping"
x-content-type-options: nosniff
date: Tue, 07 Oct 2025 20:08:10 GMT
content-length: 51
x-github-backend: Kubernetes
x-github-request-id: A000:2DC0A2:3C5671:474067:68E5732A

Affected version

Please run docker run -i --rm ghcr.io/github/github-mcp-server ./github-mcp-server --version and paste the output below

Steps to reproduce the behavior

1. Type this '...'
2. View the output '....'
3. See error

Expected vs actual behavior

A clear and concise description of what you expected to happen and what actually happened.

Logs

Paste any available logs. Redact if needed.

[tonytrg]

I tried a clean install of gemini-cli and followed the docs guidance:

$ gemini --version
0.8.2

$ cat /Users/tonytrg/.gemini/settings.json

{
  "ide": {
    "enabled": true,
    "hasSeenNudge": true
  },
  "security": {
    "auth": {
      "selectedType": "oauth-personal"
    }
  },
  "mcpServers": {
    "github": {
      "httpUrl": "https://api.githubcopilot.com/mcp/",
      "trust": true,
      "headers": {
        "Authorization": "Bearer ghp_*"
      }
    }
  }
}

And it works for me.

Note

The mcp server configuration from the UI should not be necessary, as gemini is not part of copilot managed infra, they can simply plug in the mcp server.

@SirHawbly their gemini version and a verbose log output from gemini would be nice.

Also just to make sure they are on dotcom correct?

Manual curl check

Better check to verify that the token works and they have access:

curl -X POST 'https://api.githubcopilot.com/mcp/' \
  --header 'Content-Type: application/json' \
  --data '{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "initialize"
}' \
  --header 'Authorization: Bearer ghp_*'

Output:

{
  "jsonrpc": "2.0",
  "id": 1,
  "result": {
    "protocolVersion": "2025-03-26",
    "capabilities": {
      "logging": {},
      "completion": {},
      "prompts": {},
      "resources": {
        "subscribe": true,
        "listChanged": true
      },
      "tools": {
        "listChanged": true
      }
    },
    "serverInfo": {
      "name": "github-mcp-server",
      "version": "github-mcp-server/remote-9603b8b790e9a1239fa52444237d7d224e7cce80"
    },
    "instructions": "The GitHub MCP Server provides tools to interact with GitHub platform.\n\nTool selection guidance:\n\t1. Use 'list_*' tools for broad, simple retrieval and pagination of all items of a type (e.g., all issues, all PRs, all branches) with basic filtering.\n\t2. Use 'search_*' tools for targeted queries with specific criteria, keywords, or complex filters (e.g., issues with certain text, PRs by author, code containing functions).\n\nContext management:\n\t1. Use pagination whenever possible with batches of 5-10 items.\n\t2. Use minimal_output parameter set to true if the full information is not needed to accomplish a task.\n\nTool usage guidance:\n\t1. For 'search_*' tools: Use separate 'sort' and 'order' parameters if available for sorting results - do not include 'sort:' syntax in query strings. Query strings should contain only search criteria (e.g., 'org:google language:python'), not sorting instructions. Always call 'get_me' first to understand current user permissions and context. ## Issues\n\nCheck 'list_issue_types' first for organizations to use proper issue types. Use 'search_issues' before creating new issues to avoid duplicates. Always set 'state_reason' when closing issues. ## Pull Requests\n\nPR review workflow: Always use 'create_pending_pull_request_review' → 'add_comment_to_pending_review' → 'submit_pending_pull_request_review' for complex reviews with line-specific comments."
  }
}```

[dbzix]

Have a similar problem, getting 403 with GitHub MCP.
Trying this method:

curl -i -X POST 'https://api.githubcopilot.com/mcp/' \
  --header 'Content-Type: application/json' \
  --data '{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "initialize"
}' \
  --header 'Authorization: Bearer ghp_*'

results in

HTTP/2 403 
content-security-policy: default-src 'none'; sandbox
content-type: text/plain; charset=utf-8
strict-transport-security: max-age=31536000
x-content-type-options: nosniff
date: Sat, 18 Oct 2025 12:46:42 GMT
content-length: 25
x-github-backend: Kubernetes
x-github-request-id: .................

forbidden: access denied

UPD:
This is probably due to regional restrictions (I've resided in Belarus).
After turning my VPN on, the problem is gone.