diff --git a/utils/bazel/llvm-project-overlay/clang/BUILD.bazel b/utils/bazel/llvm-project-overlay/clang/BUILD.bazel
index e85c8d758cef..b9a81797ab13 100644
--- a/utils/bazel/llvm-project-overlay/clang/BUILD.bazel
+++ b/utils/bazel/llvm-project-overlay/clang/BUILD.bazel
@@ -1455,7 +1455,11 @@ gentbl(
 # We generate the set of builtin headers under a special subdirectory in the
 # 'bin' section of the bazel output so that they can be used as data
 # dependencies. It requires listing explicitly all the generated inputs here.
-builtin_headers = glob(["lib/Headers/**/*.h"]) + [
+builtin_headers = glob(["lib/Headers/**/*.h"], exclude = [
+    # FIXME: They are not handled in CMake side.
+    "lib/Headers/openmp_wrappers/time.h",
+    "lib/Headers/ppc_wrappers/nmmintrin.h",
+]) + [
     "lib/Headers/arm_cde.h",
     "lib/Headers/arm_fp16.h",
     "lib/Headers/arm_mve.h",