Pubmed MCP Server
@cyanheads/pubmed-mcp-server Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP. Its 11 documented tools cover pubmed, articles, europepmc.
People who work with pubmed, articles and europepmc and want it reachable from Claude, Cursor, VS Code, or another MCP client. The project is written in TypeScript.
VERIFIED ACTIVE
LAST COMMIT 2026-09-13 · ★ 148 · #2 OF 71 MAINTAINED SCIENCE & HEALTH · VERIFIED 2026-09-18
Apache-2.0 · TypeScript servers · how we verify → /methodology
01 · Install Pubmed MCP Server
before you install - you'll need
Set MCP_TRANSPORT_TYPE, MCP_LOG_LEVEL, NCBI_API_KEY before connecting.
Claude Code
claude mcp add cyanheads-pubmed-mcp-server --transport http https://pubmed.caseyjhand.com/mcpClaude Desktop / Cursor / VS Code - add to config
{
"mcpServers": {
"cyanheads-pubmed-mcp-server": {
"url": "https://pubmed.caseyjhand.com/mcp"
}
}
}Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.
Using another client? Same JSON, different key
Claude Desktop · mcpServers
Cursor · mcpServers
VS Code · servers
Windsurf · mcpServers
Zed · context_servers
Cline · mcpServers
Roo Code · mcpServers
Continue · mcpServers
LibreChat · mcpServers
Gemini CLI · mcpServers
Codex CLI · mcp_servers
Full setup guides: every client.
02 · Evidence
https://pubmed.caseyjhand.com/mcp
transport: streamable-http
endpoint alive - responded to MCP initialize · probed 2026-09-17
Security posture
What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.
runs as local process (stdio) - runs on your machine with your user's permissions · remote - your agent's requests go to pubmed.caseyjhand.com
endpoint auth accepted our unauthenticated MCP initialize - no credentials needed to connect
license Apache-2.0 - declared in the repository
npm package @cyanheads/pubmed-mcp-server - published under the repo owner's npm scope (@cyanheads)
registry namespace io.github.cyanheads is GitHub-verified and matches the repo owner
03 · What Pubmed MCP Server can do
Prose above is summarized from the project's README and registry record - no invented capabilities.
What you can build
With this server connected, an agent can fetch full article metadata by PMIDs - abstract, authors, journal, MeSH terms, grants, fetch full-text articles via a chain: NCBI PMC EFetch → Europe PMC fullTextXML → Unpaywall. Accepts PMIDs, PMCIDs, or DOIs, generate formatted citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM), and find similar articles, citing articles, or references for a given PMID.
The 11 tools it gives your agent
Extracted from the project's README - what pubmed-mcp-server lets an agent do.
- pubmed_search_articles
- - Search PubMed with full query syntax, field-specific filters, date ranges, pagination, and optional brief summaries
- pubmed_europepmc_search
- - Search Europe PMC for preprints, patents, Agricola, and EPMC-only OA records that don't surface in PubMed. Cursor-based pagination.
- pubmed_europepmc_fetch
- - Fetch complete Europe PMC records - including the untruncated abstract - by source + epmcId, the only identifier many preprint, patent, and Agricola records car
- pubmed_fetch_articles
- - Fetch full article metadata by PMIDs - abstract, authors, journal, MeSH terms, grants
- pubmed_fetch_fulltext
- - Fetch full-text articles via a chain: NCBI PMC EFetch → Europe PMC fullTextXML → Unpaywall. Accepts PMIDs, PMCIDs, or DOIs.
- pubmed_format_citations
- - Generate formatted citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM)
- pubmed_find_related
- - Find similar articles, citing articles, or references for a given PMID
- pubmed_spell_check
- - Spell-check a biomedical query via NCBI ESpell - returns the corrected query and whether a suggestion was found
- pubmed_lookup_mesh
- - Search MeSH by heading - tree numbers, scope notes, entry terms - for building controlled-vocabulary queries
- pubmed_lookup_citation
- - Resolve partial bibliographic references to PubMed IDs via ECitMatch
- pubmed_convert_ids
- - Convert between DOI, PMID, and PMCID using the PMC ID Converter API
Latest releases
v2.10.13 · 2026-09-13
EFetch timeout retries, mcp-ts-core 0.13.0 adoption · NCBI EFetch backend-timeout envelopes now retry instead of failing as invalid input (#153) · Skill tree moved from skills/ to framework-skills/, so a server…
v2.10.12 · 2026-09-11
Full-text formula cleanup, APA authorless form, parser hygiene · pubmed_fetch_fulltext strips the LaTeX preamble publishers wrap around every <tex-math> formula, and renders exactly one <alternatives> child instead of…
v2.10.11 · 2026-09-11
Bookshelf records, article locators, input hardening · pubmed_fetch_articles and pubmed_format_citations return NCBI Bookshelf chapters and books with a recordType discriminator and book object, instead of reporting…
04 · Who maintains Pubmed MCP Server
pubmed-mcp-server is maintained by cyanheads. We track 125 MCP servers from cyanheads - 119 actively maintained, 1,816 combined GitHub stars, oldest repo from Dec 2024. Full record: all servers from cyanheads.
- obsidian-mcp-server Read, write, search, and surgically edit Obsidian notes, tags, and frontmatter via MCP. ★ 681
- mcp-ts-core Agent-native TypeScript framework for MCP servers. ★ 151
- git-mcp-server Comprehensive Git MCP server enabling native git tools including clone, commit, worktree, & more. ★ 240
- clinicaltrialsgov-mcp-server Search ClinicalTrials.gov - find studies, retrieve results, match patients to eligible trials. ★ 94
- ntfy-mcp-server Send, manage, and replay ntfy push notifications via MCP. ★ 22
- mcp-ts-template TypeScript template for building MCP servers with declarative tooling, observability, and auth. ★ 151
05 · Facts
- repository
- github.com/cyanheads/pubmed-mcp-server
- category
- science & health - ranked #2 of 71 actively-maintained science & health servers as of 2026-09-18.
- release cadence
- 10+ releases in the last 90 days (latest 2026-09-13)
- registry
- io.github.cyanheads/pubmed-mcp-server (active, first published 2025-09-15 · 85 versions)
- packages
- npm:@cyanheads/pubmed-mcp-server · npm:@cyanheads/pubmed-mcp-server
06 · Pubmed MCP Server FAQ
Is Pubmed MCP Server still maintained?
Yes - as of 2026-09-18, its last commit was 2026-09-13 and it shipped 10+ releases in the last 90 days. We re-verify nightly.
What can Pubmed MCP Server do?
With this server connected, an agent can fetch full article metadata by PMIDs - abstract, authors, journal, MeSH terms, grants, fetch full-text articles via a chain: NCBI PMC EFetch → Europe PMC fullTextXML → Unpaywall. Accepts PMIDs, PMCIDs, or DOIs, generate formatted citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM), and find similar articles, citing articles, or references for a given PMID.
How do I install Pubmed MCP Server?
Run `npx -y @cyanheads/pubmed-mcp-server`. The README documents 3 environment variables (MCP_TRANSPORT_TYPE, MCP_LOG_LEVEL, NCBI_API_KEY) to set first. Set MCP_TRANSPORT_TYPE, MCP_LOG_LEVEL, NCBI_API_KEY before connecting. You can also paste the ready-made client config above.
Does Pubmed MCP Server require authentication?
No - the endpoint accepted our unauthenticated MCP initialize when probed on 2026-09-17; you can connect without credentials.
07 · Alternatives to Pubmed MCP Server
Alternatives to Pubmed MCP Server
Maintained science & health servers if Pubmed MCP Server isn't the fit.
- Arxiv MCP Server (blazickjp) Search arXiv papers, download full text, semantic search, citation graphs, and alerts via MCP. ★ 3,159 · 2026-08-26
- Paper Banana Generate academic diagrams and statistical plots from text using multi-agent AI. ★ 2,367 · 2026-09-17
- Pyscn Python code analysis for AI agents: complexity, dead code, clones, coupling, and a health score. ★ 1,068 · 2026-09-17
- FHIR MCP Server MCP server providing seamless access to FHIR APIs for AI tools and healthcare applications ★ 136 · 2026-09-04
- Clinicaltrialsgov MCP Server Search ClinicalTrials.gov - find studies, retrieve results, match patients to eligible trials. ★ 94 · 2026-09-13
- Patsnap Patent & Literature Search Search 200M+ patents and 216M+ scientific papers using natural language and structured filters. ★ 79 · 2026-08-06
head to head · Arxiv MCP Server (blazickjp) vs Pubmed MCP Server · Pubmed MCP Server vs Pyscn · Clinicaltrialsgov MCP Server vs Pubmed MCP Server
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