jira_search returns empty results — uses deprecated /rest/api/3/search endpoint (HTTP 410)

[khaledfouad0]

Summary

The jira_search tool returns empty results for all queries. The response payload is:

{"total": -1, "start_at": -1, "max_results": -1, "issues": []}

This affects all JQL queries — simple (project = DEV), filtered (status = Done), sorted, paginated, etc. The jira_get_agile_boards tool also returns [].

Root Cause

Atlassian has removed the /rest/api/3/search endpoint (returns HTTP 410 Gone). The migration notice:

The requested API has been removed. Please migrate to the /rest/api/3/search/jql API. A full migration guideline is available at https://developer.atlassian.com/changelog/#CHANGE-2046

Calling the new endpoint directly with the same credentials works:

# Old endpoint — HTTP 410
curl -u user@example.com:$TOKEN "https://instance.atlassian.net/rest/api/3/search?jql=project=DEV&maxResults=1"
# → 410: {"errorMessages":["The requested API has been removed..."]}

# New endpoint — HTTP 200
curl -u user@example.com:$TOKEN "https://instance.atlassian.net/rest/api/3/search/jql?jql=project=DEV&maxResults=1"
# → 200: {"issues":[...]}

Environment

• Image: mcp/atlassian:latest (digest sha256:00ce6c4fe143ae63c28e30dd58b7e913ca1bb9dee34330fa4521b9c94b0d7d90)
• Transport: Docker MCP Gateway (stdio)
• Atlassian Cloud: Jira Cloud (team-managed project)
• Date discovered: 2026-02-20

Expected Behavior

jira_search should use the /rest/api/3/search/jql endpoint and return matching issues.

Workaround

Direct curl calls to the new /rest/api/3/search/jql endpoint work with the same credentials.

[iosamaatlassian]

We don't manage the stdio version, we only manage the remote one https://mcp.atlassian.com/v1/mcp

Incase you needed the stdio version for api tokens, We've released API Tokens for headless authentication

API Token Configuration
• Requirement: Organization admin must enable API Tokens
• Configuration guide: https://support.atlassian.com/atlassian-rovo-mcp-server/docs/configuring-authentication-via-api-token/
• Org admin enablement: https://support.atlassian.com/security-and-access-policies/docs/control-atlassian-rovo-mcp-server-settings/#Configure-authentication