diff --git a/tools/ci_build/build.py b/tools/ci_build/build.py
index 56fd3f1323e92..2080f4f7941c6 100644
--- a/tools/ci_build/build.py
+++ b/tools/ci_build/build.py
@@ -889,7 +889,7 @@ def generate_build_tree(
     # * Leave disabled if "no_kleidiai" argument was specified.
     # * Enable if the target is Android and args.android_abi contains arm64*
     # * Enable for a Windows cross compile build if compile target is an Arm one.
-    # * Finally enable if platform.machine contains "arm64". This should cover the following cases:
+    # * Finally enable if platform.machine contains "arm64" and not a WebAssembly build. This should cover the following cases:
     #     *  Linux on Arm
     #     *  MacOs (case must be ignored)
     # * TODO Delegate responsibility for Onnxruntime_USE_KLEIDIAI = ON to CMake logic
@@ -897,7 +897,7 @@ def generate_build_tree(
         if (
             (args.android and "arm64" in args.android_abi.lower())
             or (is_windows() and (args.arm64 or args.arm64ec or args.arm) and platform.architecture()[0] != "AMD64")
-            or ("arm64" in platform.machine().lower())
+            or ("arm64" in platform.machine().lower() and not args.build_wasm)
         ):
             cmake_args += ["-Donnxruntime_USE_KLEIDIAI=ON"]