Unable to establish connection between Atlassian MCP-server & github copilot in VS code

[Andew Carsten]

I tried to connect Atlassian MCP-server through github copilot in VS code but not able to do it.

"mcp": {

  "servers": {

    "atlassian": {

       "url": "https://mcp.atlassian.com/v1/sse",

       "transport": "sse",

       "command": "mcp-atlassian",

       "args": [

           "--jira-url", "https://your-company.atlassian.net",

           "--jira-username", "your.email@company.com",

           "--jira-token", "your_api_token",

           "--confluence-url", "https://your-company.atlassian.net/wiki",

           "--confluence-username", "your.email@company.com",

           "--confluence-token", "your_api_token"
        ],

      "env": {},

      "disabled": false

       }
   }
}

Tried with this code but getting this following error while running the server

2025-05-24 17:57:31.858 [info] Stopping server atlassian

2025-05-24 17:57:31.863 [info] Starting server atlassian

2025-05-24 17:57:31.864 [info] Connection state: Starting

2025-05-24 17:57:31.872 [info] Starting server from LocalProcess extension host

2025-05-24 17:57:31.875 [info] Connection state: Running

2025-05-24 17:57:32.679 [info] 401 status sending message to https://mcp.atlassian.com/v1/sse, will attempt to fall back to legacy SSE

2025-05-24 17:57:33.474 [info] Connection state: Error 401 status connecting to https://mcp.atlassian.com/v1/sse as SSE: {"error":"invalid_token","error_description":"Missing or invalid access token"}

2025-05-24 17:57:33.475 [error] Server exited before responding to `initialize` request.

Can someone provide me a solution for this.

[Fernando Nogueira]

Quiet impressive how much Atlassian is failing behind on the AI world, it's very frustrating as this prevents our company to move forward. 

[David Zhang]

same issue.

[Mark Joesting]

Same issue.

[Nikunj Manocha]

i was facing the same issue.  i was using nvm version 12.

My issue got resolved when i switched to nvm version 18. Any other version lower than that I kept getting some error.

please try and update if this resolves your error.

[afenn]

I'm on 0.39.0 and it still does not work.

[dean.pullen]

Same issue.

[afenn]

Still the same issue. Come on Atlassian.. 

[Dave]

Same here

[Hernan Montes]

I have been working with the MCP server, unfortunately, while investigating, I came to the conclusion that plain API keys will not work, you need to use a JWT token, which needs to he provided while processing handshakes with the MCP server, then you can use the approved token to connect woth your code.

[Ronny Katzenberger]

Merry Christmas - same issue. It's been working somewhat stable as in "you only had to restart the server" but then it degrades into the invalid_token state and I'm not sure how to fix that. I had this before, and had it resolved - no idea what combination of uninstalling the Atlassian MCP Server or other steps fixed it for me, at least temporarily.