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 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?