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FHIR MCP Server

Name: FHIR MCP Server MCP Server
Author: the-momentum

by the-momentum · the-momentum/fhir-mcp-server

Query and write to any FHIR-compliant healthcare server via MCP.

FHIR (Fast Healthcare Interoperability Resources) is the standard API for clinical data. This MCP lets Claude query any FHIR server — patient records, observations, medications — and follow the spec's resource references like a real EHR app.

▶ Watch demo 📦 Install 💡 Use Cases

Why use it

Key features

All FHIR R4/R5 resource types: Patient, Observation, MedicationRequest, etc.
Search by parameter (date range, code, identifier)
Reference traversal — follow Patient → Observation → Encounter chains
Bulk export for cohort queries
Works against any FHIR server (Epic, Cerner sandbox, HAPI, Aidbox)

Live Demo

What it looks like in practice

fhir-mcp-server.replay ▶ ready

0/0

Install

Pick your client

~/Library/Application Support/Claude/claude_desktop_config.json · Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "fhir-mcp-server": {
      "command": "uvx",
      "args": [
        "fhir-mcp-server"
      ]
    }
  }
}

Open Claude Desktop → Settings → Developer → Edit Config. Restart after saving.

~/.cursor/mcp.json · .cursor/mcp.json

{
  "mcpServers": {
    "fhir-mcp-server": {
      "command": "uvx",
      "args": [
        "fhir-mcp-server"
      ]
    }
  }
}

Cursor uses the same mcpServers schema as Claude Desktop. Project config wins over global.

VS Code → Cline → MCP Servers → Edit

{
  "mcpServers": {
    "fhir-mcp-server": {
      "command": "uvx",
      "args": [
        "fhir-mcp-server"
      ]
    }
  }
}

Click the MCP Servers icon in the Cline sidebar, then "Edit Configuration".

~/.codeium/windsurf/mcp_config.json

{
  "mcpServers": {
    "fhir-mcp-server": {
      "command": "uvx",
      "args": [
        "fhir-mcp-server"
      ]
    }
  }
}

Same shape as Claude Desktop. Restart Windsurf to pick up changes.

~/.continue/config.json

{
  "mcpServers": [
    {
      "name": "fhir-mcp-server",
      "command": "uvx",
      "args": [
        "fhir-mcp-server"
      ]
    }
  ]
}

Continue uses an array of server objects rather than a map.

~/.config/zed/settings.json

{
  "context_servers": {
    "fhir-mcp-server": {
      "command": {
        "path": "uvx",
        "args": [
          "fhir-mcp-server"
        ]
      }
    }
  }
}

Add to context_servers. Zed hot-reloads on save.

claude mcp add fhir-mcp-server -- uvx fhir-mcp-server

One-liner. Verify with claude mcp list. Remove with claude mcp remove.

Use Cases

Real-world ways to use FHIR MCP Server

Build a chronological clinical timeline for one patient

👤 Clinical informatics, research teams ⏱ ~15 min intermediate

When to use: You need a summary of one patient's encounters, meds, and labs across visits.

Prerequisites

Server/skill installed and authenticated — See repo README

Flow

Get the patient

Find Patient with identifier MRN-12345 and return name, DOB, and active conditions.✓ Copied

→ One Patient + Condition list
Build the timeline

Retrieve all Encounters and MedicationRequests for that patient in the last 12 months. Sort chronologically and summarize.✓ Copied

→ Time-sorted list with encounter type + meds prescribed

Outcome: A clinician-readable summary you can paste into a chart note.

Pitfalls

Real PHI — Real PHI — never connect this to a chat that's also pasting screenshots to a third-party service. Use a HIPAA-compliant Claude deployment.

Combine with: filesystem · memory

Combinations

Pair with other MCPs for X10 leverage

fhir-mcp-server + filesystem

Pair with filesystem for complementary capabilities

Use this server together with filesystem to complete a multi-step task.✓ Copied

fhir-mcp-server + memory

Pair with memory for complementary capabilities

Use this server together with memory to complete a multi-step task.✓ Copied

Tools

What this MCP exposes

Tool	Inputs	When to call	Cost
fhir_search	resource_type, params	Find resources matching criteria	1 API call
fhir_read	resource_type, id	Read one specific resource	1 API call
fhir_create	resource_type, body	Write a new clinical resource	1 API call

Cost & Limits

What this costs to run

API quota: See provider docs for rate limits
Tokens per call: Varies by tool
Monetary: See repo README for pricing details
Tip: Cache tool results and avoid repeated identical calls.

Security

Permissions, secrets, blast radius

Credential storage: Use environment variables; never commit secrets

Data egress: Tool calls go to the provider's API as documented

Troubleshooting

Common errors and fixes

401 from FHIR server

Most FHIR servers use SMART-on-FHIR. Generate a token via your EHR's auth flow and set FHIR_TOKEN.

Verify: fhir_search Patient?_count=1 returns a Bundle

Unsupported resource type

Different servers implement different subsets. Check the CapabilityStatement: GET /metadata.

Verify: Confirm the resource type is in CapabilityStatement.rest.resource

Alternatives

FHIR MCP Server vs others

Alternative	When to use it instead	Tradeoff
wso2/fhir-mcp-server	You're on the WSO2 stack	Tighter WSO2 integration

Resources

📖 Read the official README on GitHub

🐙 Browse open issues

🔍 Browse all 400+ MCP servers and Skills