Codex mcp connection error

[Skyline-23]

Describe the bug

When try to connect mcp in codex, error occurred

Affected version

codex version 0.73.0
github remote server mcp

Steps to reproduce the behavior

edit config.toml, and run codex

Expected vs actual behavior

⚠ MCP client for `github` failed to start: MCP startup failed: Environment
  variable
  github_pat_(token) for MCP server 'github' is not set

⚠ MCP startup incomplete (failed: github)

Here is my my config.toml

[mcp_servers.github]
url = "https://api.githubcopilot.com/mcp/"
bearer_token_env_var = "github_pat_(token)"

[javiertorne]

Same here. Do you find a solution?

[Skyline-23]

@javiertorne nope... It still shows everytime when start codex session

[javiertorne]

@Skyline-23 I found a solution. put your token inside an .env file in the project directory.

the content of the file has to be something like that:

GITHUB_PAT_TOKEN=<ghp_yourtoken>

then, in your congif.toml, put this:

[mcp_servers.github]
url = "https://api.githubcopilot.com/mcp/"
bearer_token_env_var = "GITHUB_PAT_TOKEN"

doing this, it works but you have to set the variable every time you open a new terminal window in the project doing:
set -a
source .env
set +a

so I created an alias to do it automatically:
alias e="cd ~/myProject && set -a && source .env && set +a"

remember to add the .env file to your gitignore to not expose your token.

hope it helps

[tommaso-moro]

Closing this as it has been solved (thank you @javiertorne ). Note that the Codex installation guide is also available in our official docs: https://github.com/github/github-mcp-server/blob/main/docs/installation-guides/install-codex.md

Please let me know if you think the guide is out of date or if you are still experiencing issues with this!

[HaochenFa]

Thanks @javiertorne . Sorry for interrupting a closed issue, but I think there's a way that we don't have to source .env everytime — export the PAT token in your shell environment.

E.g., (I use zsh) in .zshrc

export GITHUB_PAT_TOKEN="ghp_XXXXXXXXXXX"

then

source .zshrc

In .codex/config.toml,

[mcp_servers.github]
url = "https://api.githubcopilot.com/mcp/"
# Replace with your real PAT (least-privilege scopes). Do NOT commit this.
bearer_token_env_var = "GITHUB_PAT_TOKEN"

That works on my computer. Hope this can help any other people who encountered the same issue.

[dimentary]

This is not a proper solution but rather a workaround, Following the Github guide won't make it work unless "Storing Your PAT Securely" subsection is done.

[JuGit-pk]

Thanks @javiertorne for the helpful approach.

Easy steps that worked for me:

1. Put your token variable in ~/.codex/.env (example: GITHUB_PAT_TOKEN=ghp_xxx).
2. Add this to .zshrc:

codexenv() {
  local env_file="$HOME/.codex/.env"
  [[ -f "$env_file" ]] || return 0
  set -a
  source "$env_file"
  set +a
}

codexenv

3. In ~/.codex/config.toml, set bearer_token_env_var to the same variable name from ~/.codex/.env.
4. Open a new terminal (or reload zsh).

After this, MCP connected correctly for me.

[rirze]

This is an god-forsaken absolutely awful workflow for codex.

I barely understand the security angle in not storing Github PAT in codex config (ok, great, we now store it global shell config or project-specific .env files-- How does that make security any better?). Even if we wanted to bypass this by storing it as an env var in codex config:

[mcp_servers.github]
url = "https://api.githubcopilot.com/mcp/"
bearer_token_env_var = "GITHUB_PAT"

[mcp_servers.github.env]
GITHUB_PAT = "github_pat_..."

codex fails to start up with

Error loading config.toml: env is not supported for streamable_http
in `mcp_servers.github`

So now, I read this issue and the recommendation is to commit some shell-fu to be able to use Github MCP with codex?

I decline. Thank god for http_headers override:

[mcp_servers.github]
url = "https://api.githubcopilot.com/mcp/"
http_headers = { "Authorization" = "github_pat_....." }

This should be the recommended workflow 👆