diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index fe0b9827f..e32be0f58 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -31,7 +31,7 @@ repos:
           - types-requests==2.32.4.20250913
           - types-tabulate==0.9.0.20241207
           - types-python-dateutil==2.9.0.20251008
-          - scipy-stubs==1.16.2.4
+          - scipy-stubs==1.16.3.0
           - SQLAlchemy==2.0.44
         # stages: [push]
 
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 970ba024b..c36888767 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -24,7 +24,7 @@ time-machine==2.19.0
 nbconvert==7.16.6
 
 # mypy types
-scipy-stubs==1.16.2.4  # keep in sync with `scipy` in `requirements-hyperopt.txt`
+scipy-stubs==1.16.3.0  # keep in sync with `scipy` in `requirements-hyperopt.txt`
 types-cachetools==6.2.0.20251022
 types-filelock==3.2.7
 types-requests==2.32.4.20250913
diff --git a/requirements-hyperopt.txt b/requirements-hyperopt.txt
index 49fdecd7d..6b777b47b 100644
--- a/requirements-hyperopt.txt
+++ b/requirements-hyperopt.txt
@@ -2,7 +2,7 @@
 -r requirements.txt
 
 # Required for hyperopt
-scipy==1.16.2
+scipy==1.16.3
 scikit-learn==1.7.2
 filelock==3.20.0
 optuna==4.5.0