diff --git a/.ci/docker/requirements-ci.txt b/.ci/docker/requirements-ci.txt
index efc058b1d375e..3d3746535aee9 100644
--- a/.ci/docker/requirements-ci.txt
+++ b/.ci/docker/requirements-ci.txt
@@ -160,8 +160,8 @@ pillow==11.0.0
 #Description:  Python Imaging Library fork
 #Pinned versions: 10.3.0
 #test that import:
-
-protobuf==3.20.2
+protobuf==3.20.2 ; python_version <= "3.12"
+protobuf==4.25.1 ; python_version == "3.13"
 #Description:  Google’s data interchange format
 #Pinned versions: 3.20.1
 #test that import: test_tensorboard.py
@@ -324,7 +324,8 @@ pywavelets==1.7.0 ; python_version >= "3.12"
 #Pinned versions: 1.4.1
 #test that import:
 
-lxml==5.3.0
+lxml==5.3.0 ; python_version <= "3.12"
+lxml==6.0.0 ; python_version == "3.13"
 #Description: This is a requirement of unittest-xml-reporting
 
 # Python-3.9 binaries
@@ -336,7 +337,8 @@ sympy==1.13.1 ; python_version >= "3.9"
 #Pinned versions:
 #test that import:
 
-onnx==1.17.0
+onnx==1.16.1 ; python_version <= "3.12"
+onnx==1.18.0 ; python_version == "3.13"
 #Description: Required by mypy and test_public_bindings.py when checking torch.onnx._internal
 #Pinned versions:
 #test that import: