diff --git a/tools/ep_kernels/install_python_libraries.sh b/tools/ep_kernels/install_python_libraries.sh
index 77af3f68a0505..1cea1bef8dbc9 100755
--- a/tools/ep_kernels/install_python_libraries.sh
+++ b/tools/ep_kernels/install_python_libraries.sh
@@ -96,6 +96,13 @@ clone_repo() {
     fi
 }
 
+deepep_cuda13_patch() {
+    cuda_version_major=$(${CUDA_HOME}/bin/nvcc --version | egrep -o "release [0-9]+" | cut -d ' ' -f 2)
+    if [ ${cuda_version_major} -ge 13 ]; then
+        sed -i "s|f'{nvshmem_dir}/include']|f'{nvshmem_dir}/include', '${CUDA_HOME}/include/cccl']|" "setup.py"
+    fi
+}
+
 do_build() {
     local repo=$1
     local name=$2
@@ -107,6 +114,10 @@ do_build() {
     clone_repo "$repo" "$name" "$key" "$commit"
     cd "$name"
 
+    if [ "$name" == "DeepEP" ]; then
+        deepep_cuda13_patch
+    fi
+
     if [ "$MODE" = "install" ]; then
         echo "Installing $name into environment"
         eval "$extra_env" uv pip install --no-build-isolation -vvv .