diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f12831164..0c0e76879 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -31,6 +31,7 @@ repos:
           - types-requests==2.32.4.20250611
           - types-tabulate==0.9.0.20241207
           - types-python-dateutil==2.9.0.20250516
+          - scipy-stubs==1.15.3.0
           - SQLAlchemy==2.0.41
         # stages: [push]
 
diff --git a/build_helpers/pre_commit_update.py b/build_helpers/pre_commit_update.py
index 9d313efd2..9e49aa7c2 100644
--- a/build_helpers/pre_commit_update.py
+++ b/build_helpers/pre_commit_update.py
@@ -16,10 +16,12 @@ with require_dev.open("r") as rfile:
 with require.open("r") as rfile:
     requirements.extend(rfile.readlines())
 
-# Extract types only
-type_reqs = [
-    r.strip("\n") for r in requirements if r.startswith("types-") or r.startswith("SQLAlchemy")
-]
+# Extract relevant types only
+supported = ("types-", "SQLAlchemy", "scipy-stubs")
+
+# Find relevant dependencies
+# Only keep the first part of the line up to the first space
+type_reqs = [r.strip("\n").split()[0] for r in requirements if r.startswith(supported)]
 
 with pre_commit_file.open("r") as file:
     f = yaml.load(file, Loader=yaml.SafeLoader)
diff --git a/pyproject.toml b/pyproject.toml
index eb626ac81..df6048cb6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -111,6 +111,7 @@ develop = [
   "pytest-xdist",
   "pytest",
   "ruff",
+  "scipy-stubs",
   "time-machine",
   "types-cachetools",
   "types-filelock",
diff --git a/requirements-dev.txt b/requirements-dev.txt
index c597f9b8a..90d1ba2fa 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -24,6 +24,7 @@ time-machine==2.16.0
 nbconvert==7.16.6
 
 # mypy types
+scipy-stubs==1.15.3.0  # keep in sync with `scipy` in `requirements-hyperopt.txt`
 types-cachetools==6.0.0.20250525
 types-filelock==3.2.7
 types-requests==2.32.4.20250611