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How to add FHIR MCP Server to Claude Desktop

Expose any FHIR server or API as MCP tools to search, read, and write clinical data with SMART-on-FHIR auth. Paste the config into ~/Library/Application Support/Claude/claude_desktop_config.json and restart Claude Desktop.

Last updated June 14, 2026 · 124★ · stdio · oauth · official

Claude Desktop config for FHIR MCP Server

uvx fhir-mcp-server
{
  "mcpServers": {
    "fhir-mcp-server": {
      "command": "uv",
      "args": [
        "--directory",
        "/path/to/fhir-mcp-server",
        "run",
        "fhir-mcp-server",
        "--transport",
        "stdio"
      ],
      "env": {
        "FHIR_SERVER_ACCESS_TOKEN": "Your FHIR Access Token"
      }
    }
  }
}

Setup steps

  1. 1Open Claude Desktop → Settings → Developer → Edit Config (this opens ~/Library/Application Support/Claude/claude_desktop_config.json).
  2. 2Paste the FHIR MCP Server config below under the top-level "mcpServers" key.
  3. 3Fill in any placeholder secrets (API keys, paths) in the snippet.
  4. 4Save the file, then fully quit and reopen Claude Desktop.
  5. 5Open a chat and confirm FHIR MCP Server's tools appear under the 🔌 tools menu.

Before you start

  • Python 3.8+
  • uv (for dependency management)
  • An accessible FHIR API server (e.g. HAPI FHIR, Epic sandbox)

What FHIR MCP Server can do in Claude Desktop

get_capabilities

Retrieves metadata about a specified FHIR resource type, including its supported search parameters and custom operations. Parameter: type (FHIR resource type name, e.g. Patient, Observation, Encounter).

search

Executes a standard FHIR search interaction on a given resource type, returning a bundle or list of matching resources. Parameters: type, searchParam (map of search parameter names to values), and optional response_filter_fhirpaths (array of FHIRPath expressions to filter the response bundle).

read

Performs a FHIR read interaction to retrieve a single resource instance by type and resource ID, optionally refined with search parameters or custom operations (e.g. $everything). Parameters: type, id, searchParam, operation, and optional response_filter_fhirpaths.

create

Executes a FHIR create interaction to persist a new resource of the specified type. Parameters: type, payload (full FHIR resource body), searchParam, and operation (e.g. $evaluate).

update

Performs a FHIR update interaction by replacing an existing resource instance's content with the provided payload. Parameters: type, id, payload, searchParam, and operation (e.g. $lastn).

delete

Executes a FHIR delete interaction on a specific resource instance. Parameters: type, id, searchParam, and operation (e.g. $expand).

get_user

Retrieves the currently authenticated user's FHIR resource (e.g. the linked Patient resource) and returns a concise profile with available demographic fields such as id, name, and birthDate. Requires the fhirUser and openid scopes.

Security

Uses SMART-on-FHIR / OAuth 2.0 authorization code grant by default; configure FHIR_SERVER_CLIENT_ID, FHIR_SERVER_CLIENT_SECRET, and FHIR_SERVER_SCOPES, or set FHIR_SERVER_ACCESS_TOKEN to use a token directly. Set FHIR_SERVER_DISABLE_AUTHORIZATION=True for public FHIR servers. The README notes that when running locally via Docker or Docker Compose, authorization should currently be disabled (FHIR_SERVER_DISABLE_AUTHORIZATION=True) pending a future fix. Handles protected health information (PHI) — secure FHIR credentials and access tokens accordingly.

FHIR MCP Server + Claude Desktop FAQ

Where is the Claude Desktop config file?

Claude Desktop reads MCP servers from ~/Library/Application Support/Claude/claude_desktop_config.json. Paste the FHIR MCP Server config there under the "mcpServers" key and restart the client.

Is FHIR MCP Server safe to use with Claude Desktop?

Uses SMART-on-FHIR / OAuth 2.0 authorization code grant by default; configure FHIR_SERVER_CLIENT_ID, FHIR_SERVER_CLIENT_SECRET, and FHIR_SERVER_SCOPES, or set FHIR_SERVER_ACCESS_TOKEN to use a token directly. Set FHIR_SERVER_DISABLE_AUTHORIZATION=True for public FHIR servers. The README notes that when running locally via Docker or Docker Compose, authorization should currently be disabled (FHIR_SERVER_DISABLE_AUTHORIZATION=True) pending a future fix. Handles protected health information (PHI) — secure FHIR credentials and access tokens accordingly.

Which FHIR servers does it work with?

Any accessible FHIR API server. The README demonstrates a public HAPI FHIR server (no auth flow needed) and the Epic EHR sandbox (full OAuth 2.0 authorization code grant). Set FHIR_SERVER_BASE_URL to the target server.

How is authentication handled?

It uses SMART-on-FHIR / OAuth 2.0 authorization code grant by default (configure FHIR_SERVER_CLIENT_ID, FHIR_SERVER_CLIENT_SECRET, FHIR_SERVER_SCOPES). You can bypass the flow by setting FHIR_SERVER_ACCESS_TOKEN directly, or disable authorization entirely with FHIR_SERVER_DISABLE_AUTHORIZATION=True for public servers.

What transports are supported?

stdio, SSE, and streamable HTTP. The default transport is streamable-http; choose with the --transport CLI flag. By default the server listens on http://localhost:8000.

View repo Full FHIR MCP Server page