diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index f1aff439037..99c72662cce 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -318,9 +318,6 @@ class ConditionalDependencies:
             self.config.get("ai_api_key", None) is not None or self.config.get("inference_services", None) is not None
         )
 
-    def check_fastmcp(self):
-        return asbool(self.config.get("enable_mcp_server", False))
-
     def check_weasyprint(self):
         # See notes in ./conditional-requirements.txt for more information.
         return os.environ.get("GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT") == "1"
diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index 5ddb0f37b26..e1a5ef8577c 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -16,7 +16,6 @@ galaxycloudrunner
 pkce
 total-perspective-vortex>=3.2.1,<4
 openai
-fastmcp>=2.13.0
 # upper version constraint because of https://github.com/galaxyproject/galaxy/issues/20600
 redis>=5.3.0,<6
 
diff --git a/lib/galaxy/webapps/galaxy/fast_app.py b/lib/galaxy/webapps/galaxy/fast_app.py
index f6440ca03af..f4e386d654a 100644
--- a/lib/galaxy/webapps/galaxy/fast_app.py
+++ b/lib/galaxy/webapps/galaxy/fast_app.py
@@ -36,6 +36,7 @@ from galaxy.webapps.base.webapp import (
     _is_embed_request,
     config_allows_origin,
 )
+from galaxy.webapps.galaxy.api.mcp import get_mcp_app
 from galaxy.webapps.openapi._compat.v2 import GenerateJsonSchema
 from galaxy.webapps.openapi.utils import get_openapi
 
@@ -267,13 +268,8 @@ def get_mcp_lifespan(gx_app):
         return None, None
 
     try:
-        from galaxy.webapps.galaxy.api.mcp import get_mcp_app
-
         mcp_app = get_mcp_app(gx_app)
         return mcp_app, mcp_app.lifespan
-    except ImportError:
-        log.info("MCP server dependencies not installed (fastmcp), skipping")
-        return None, None
     except Exception:
         log.exception("Failed to initialize MCP server")
         return None, None
diff --git a/packages/web_apps/pyproject.toml b/packages/web_apps/pyproject.toml
index bafb9f424a8..da8f1c02847 100644
--- a/packages/web_apps/pyproject.toml
+++ b/packages/web_apps/pyproject.toml
@@ -28,6 +28,7 @@ dependencies = [
     "Babel",
     "CT3>=3.3.3",
     "fastapi>=0.133.0",
+    "fastmcp>=2.13.0",
     "gunicorn!=25.1.0",
     "httpx",
     "gxformat2>=0.27.0",
diff --git a/pyproject.toml b/pyproject.toml
index ea38192daef..bcef73cf3be 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,6 +38,7 @@ dependencies = [
     "dparse",
     "edam-ontology",
     "fastapi>=0.133.0",  # First version compatible with starlette>=1.0.0
+    "fastmcp>=2.13.0",
     "fissix",
     "fs",
     "future>=1.0.0",  # Python 3.12 support