Atlassian MCP Server vs Self Hosted GitHub MCP server

In-depth architectural comparison of the Atlassian MCP Server and Self Hosted GitHub MCP server MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.

Which MCP Server Should You Choose?

Choose Atlassian MCP Server when:

• You need dedicated capabilities in the Version Control domain.
• You prefer remote streaming HTTP/SSE transport architecture.
• Your security boundary fits: other (Free / Open Source).
• Primary tools included: Remote MCP endpoint hosted by Atlassian, OAuth 2.1 and API token authentication, Jira and Confluence access.

Explore Atlassian MCP Server Details

Choose Self Hosted GitHub MCP server when:

• You need dedicated capabilities in the Version Control domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).
• Primary tools included: health_check, list_prs, get_pr.

Explore Self Hosted GitHub MCP server Details

Feature & Specification Comparison

Specification	Atlassian MCP Server VerifiedVersion Control	Self Hosted GitHub MCP server Version Control
Summary	Official remote MCP server for Atlassian. Securely connect Jira, Confluence, Jira Service Management, Bitbucket, and Compass to Claude, ChatGPT, Cursor, VS Code, and other AI tools using OAuth 2.1 or API tokens.	Self-hosted GitHub MCP server. PAT auth, stdio transport, transport-agnostic so it works with…
Category & Scope

Tools & Capabilities Breakdown

Ready-to-Paste Client Configurations

Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).

{
  "mcpServers": {
    "atlassian-mcp-server": {
      "url": "https://mcp.atlassian.com/v2/mcp"
    }
  }
}

{
  "mcpServers": {
    "self-hosted-github-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "self-hosted-github-mcp-server"
      ]
    }
  }
}

Related MCP Server Comparisons