Unstable Atlassian MCP Server Connection

[Yusian Li]

We are using Claude Code to connect to the Atlassian MCP server and have encountered two intermittent issues.

(Atl-Request-Id are attached, hopefully Atlassian team can help doing further investigation.)

Environment

• Client: Claude Code (v2.1.17)
• MCP Server: mcp.atlassian.com

Issue 1: 401 Unauthorized After Token Refresh

Sometimes receive a 401 Unauthorized error in the response body despite using a freshly refreshed token (token lifetime: 3300s).

Request logs:

code  method  host    path    start   info

200   POST    cf.mcp.atlassian.com    /v1/token       Fri Jan 23 02:01:42 UTC 2026    Token refresh

200   POST    mcp.atlassian.com       /v1/mcp Fri Jan 23 02:32:58 UTC 2026    tools/call

response: event: message

  data: {"result":{"isError":false,"content":[{"type":"text","text":"{\"code\":401,\"message\":\"Unauthorized\"}"}]},"jsonrpc":"2.0","id":8}

Atl-Request-Id 024a0ed7-be0a-4594-a9e5-08ee8c05d500

Issue 2: "Session not found" Error

Intermittently receiving a 404 response with "Session not found" error. Re-initializing (via Claude Code /mcp reconnect) the MCP connection resolves the issue temporarily.

Request logs:

code  method  host    path    start   info

200   POST    cf.mcp.atlassian.com    /v1/token       Fri Jan 23 03:54:58 UTC 2026    Token refresh

404   POST    mcp.atlassian.com       /v1/mcp Fri Jan 23 03:55:30 UTC 2026    tools/call (session not found)

response: {"jsonrpc":"2.0","error":{"code":-32001,"message":"Session not found"}}

Atl-Request-Id: 7779c0e5-aeca-4d92-927d-e5b7e9714d68

200   POST    mcp.atlassian.com       /v1/mcp Fri Jan 23 03:56:19 UTC 2026    initialize

200   POST    mcp.atlassian.com       /v1/mcp Fri Jan 23 03:56:31 UTC 2026    tools/call (success)

Atl-Request-Id f70a6671-27cd-4979-b3e8-56cda0d054db

Has anyone else experienced the same issues?

[Tomislav Tobijas]

Hi @Yusian Li ,

I'm guessing that you've already gone through the official docs for setting up Claude. You could also check the following article Troubleshooting and verifying your setup as it might help you troubleshoot the issue you're experiencing.

I haven't integrated Claude myself, so I can't say much, but a recommendation would also be to check this forum discussion group: Atlassian Rovo MCP Server 

Generally speaking:

• 401 Unauthorized After Token Refresh > auth failure (due to expired token, missing OAuth scopes...); trigger new login by re-running connection flow
• "Session not found" Error (404) > usually means MCP session has expired or become invalid (could be related to 401 error)

Hope you'll get this resolved.

Cheers,
Tobi

[Yusian Li]

Thank you Tobi! And yes, re-auth and reconnect did help, but ran into the same few hours later. Those Intermittent issues affect user experience a lot. Not sure if there is something can be done at Atlassian side.

[Tomislav Tobijas]

@Yusian Li definitelly not a friendly UI :/

You could also check with Dev community to see if the folks there have any insights about this constant reconnecting 👀