Clinicaltrialsgov MCP Server vs Pubmed MCP Server
Two MCP servers from our science & health ranking, compared on live data - updated nightly, never sponsored.
Bottom line · 2026-09-18
monthly package install counts are comparable (9,456 vs 13,671); both are actively maintained, with commits inside the last month.
How they differ in kind
Clinicaltrialsgov MCP Server focuses on: clinicaltrialsgov-mcp-server Search ClinicalTrials.gov trials, retrieve study details and results, and match patients to eligible trials via MCP. Pubmed MCP Server focuses on: @cyanheads/pubmed-mcp-server Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. Tool coverage differs: Clinicaltrialsgov MCP Server documents 7 tools (including clinicaltrials_search_studies, clinicaltrials_get_study_record, clinicaltrials_get_study_count, clinicaltrials_get_field_values); Pubmed MCP Server documents 11 (including pubmed_search_articles, pubmed_europepmc_search, pubmed_europepmc_fetch, pubmed_fetch_articles). Environment-variable extraction: Clinicaltrialsgov MCP Server yielded 2 variables; Pubmed MCP Server yielded 3 variables.
What each one does
Clinicaltrialsgov MCP Server
clinicaltrialsgov-mcp-server Search ClinicalTrials.gov trials, retrieve study details and results, and match patients to eligible trials via MCP. STDIO or Streamable HTTP. Its 7 documented tools cover clinicaltrials, study.
From the project's README.
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.
From the project's README.
14 signals, side by side
| Signal | Clinicaltrialsgov MCP Server | Pubmed MCP Server |
|---|---|---|
| Monthly installs | 9,456 | 13,671 |
| GitHub stars | 94 | 148 |
| Last commit | 2026-09-13 | 2026-09-13 |
| Releases · last 90 days | 10+ | 10+ |
| In the registry since | Oct 2025 | Sep 2025 |
| Registry versions | 69 | 85 |
| Documented tools | 7 | 11 |
| Env vars extracted | 2 | 3 |
| Runs | local or remote | local or remote |
| Endpoint auth | none (verified open) | none (verified open) |
| Maintenance | actively maintained | actively maintained |
| License | Apache-2.0 | Apache-2.0 |
| Language | TypeScript | TypeScript |
| Category rank | #4 of 71 | #2 of 71 |
What their tools cover
Extracted from each project's README - the tools each server hands your agent. A missing list means the README doesn't document one, not that no tools exist.
Clinicaltrialsgov MCP Server 7 tools documented
clinicaltrials_search_studies- Search studies with full-text and field-specific queries…clinicaltrials_get_study_record- Fetch a single study by NCT ID - full protocol record with optional…clinicaltrials_get_study_count- Fast total study count for a query, without fetching dataclinicaltrials_get_field_values- Discover valid values for API fields, with per-value study countsclinicaltrials_get_field_definitions- Resolve valid field names - keyword search, path drill-down, or…clinicaltrials_get_study_results- Fetch posted results - outcomes, adverse events, participant flow…clinicaltrials_find_eligible- Match patient demographics and conditions to eligible recruiting…
Pubmed MCP Server 11 tools documented
pubmed_search_articles- Search PubMed with full query syntax, field-specific filters, date…pubmed_europepmc_search- Search Europe PMC for preprints, patents, Agricola, and EPMC-only OA…pubmed_europepmc_fetch- Fetch complete Europe PMC records - including the untruncated…pubmed_fetch_articles- Fetch full article metadata by PMIDs - abstract, authors, journal…pubmed_fetch_fulltext- Fetch full-text articles via a chain: NCBI PMC EFetch → Europe PMC…pubmed_format_citations- Generate formatted citations in APA 7th, MLA 9th, BibTeX, RIS, or…pubmed_find_related- Find similar articles, citing articles, or references for a given PMIDpubmed_spell_check- Spell-check a biomedical query via NCBI ESpell - returns the…
+3 more on the full page
Environment variables found in the READMEs
These are extracted names, not a requiredness check. Project docs may mark them optional or require other setup.
Clinicaltrialsgov MCP Server
- MCP_TRANSPORT_TYPE
- MCP_LOG_LEVEL
Pubmed MCP Server
- MCP_TRANSPORT_TYPE
- MCP_LOG_LEVEL
- NCBI_API_KEY
Which one, for what
Derived from the signals above, not hands-on testing.
Pick Clinicaltrialsgov MCP Server if…
- → its documented toolset fits - 7 tools including clinicaltrials_search_studies, clinicaltrials_get_study_record
- → category standing - #4 of 71 maintained science & health servers
Pick Pubmed MCP Server if…
- → its documented toolset fits - 11 tools including pubmed_search_articles, pubmed_europepmc_search
- → measured package adoption matters - 13,671 monthly installs
Who's behind them
Clinicaltrialsgov MCP Server - cyanheads: 125 MCP servers tracked, 119 maintained, 1,816 combined stars. Full record.
Pubmed MCP Server - cyanheads: 125 MCP servers tracked, 119 maintained, 1,816 combined stars. Full record.
Not sold on either?
The next-ranked science & health servers we track:
Quick answers
Is Clinicaltrialsgov MCP Server better than Pubmed MCP Server?
The numbers don't separate them: 9,456 vs 13,671 monthly installs, and both committed within the last month. Choose on fit - execution model, extracted environment variables, endpoint authentication, and license are in the table above. Data as of 2026-09-18.
Can I use Clinicaltrialsgov MCP Server and Pubmed MCP Server together?
Yes - MCP clients accept multiple servers in one config, so you can enable both science & health servers side by side. If their tools overlap, keep the one whose toolset fits to keep your agent's tool list lean.
What environment variables do their READMEs document?
Clinicaltrialsgov MCP Server: 2 environment variables extracted from the README setup; Pubmed MCP Server: 3 environment variables extracted from the README setup. Extraction does not rule out other authentication or configuration steps; check each project's current documentation.
Keep exploring: best science & health servers · TypeScript servers · all comparisons · every server
Methodology: package-usage signal = npm/PyPI installs (last month, platform APIs) · maintenance = commit recency + release cadence (GitHub) · tool lists and environment-variable names extracted from each project's README · endpoint auth from our own nightly probes. We haven't hand-tested these servers; everything here is data as of 2026-09-18.