diff --git a/onnxruntime/core/providers/webgpu/buffer_manager.h b/onnxruntime/core/providers/webgpu/buffer_manager.h
index 20bee52835c02..a5bba53c6798b 100644
--- a/onnxruntime/core/providers/webgpu/buffer_manager.h
+++ b/onnxruntime/core/providers/webgpu/buffer_manager.h
@@ -5,7 +5,7 @@
 
 #include <iosfwd>
 
-#include <webgpu/webgpu_cpp.h>
+#include "core/providers/webgpu/webgpu_external_header.h"
 
 #include "core/framework/execution_provider.h"
 
diff --git a/onnxruntime/core/providers/webgpu/compute_context.h b/onnxruntime/core/providers/webgpu/compute_context.h
index 680e03aef0aa3..23fa10a0d5489 100644
--- a/onnxruntime/core/providers/webgpu/compute_context.h
+++ b/onnxruntime/core/providers/webgpu/compute_context.h
@@ -3,7 +3,7 @@
 
 #pragma once
 
-#include <webgpu/webgpu_cpp.h>
+#include "core/providers/webgpu/webgpu_external_header.h"
 
 #include <utility>
 
diff --git a/onnxruntime/core/providers/webgpu/program_manager.h b/onnxruntime/core/providers/webgpu/program_manager.h
index 55721770014d2..feeb703b95aa2 100644
--- a/onnxruntime/core/providers/webgpu/program_manager.h
+++ b/onnxruntime/core/providers/webgpu/program_manager.h
@@ -6,7 +6,7 @@
 #include <string>
 #include <unordered_map>
 
-#include <webgpu/webgpu_cpp.h>
+#include "core/providers/webgpu/webgpu_external_header.h"
 
 #include "core/common/common.h"
 
diff --git a/onnxruntime/core/providers/webgpu/shader_helper.h b/onnxruntime/core/providers/webgpu/shader_helper.h
index dac08f3bd9368..64b4c054f93d4 100644
--- a/onnxruntime/core/providers/webgpu/shader_helper.h
+++ b/onnxruntime/core/providers/webgpu/shader_helper.h
@@ -5,7 +5,7 @@
 
 #include <sstream>
 
-#include <webgpu/webgpu_cpp.h>
+#include "core/providers/webgpu/webgpu_external_header.h"
 
 #include "core/framework/tensor_shape.h"
 
diff --git a/onnxruntime/core/providers/webgpu/webgpu_context.h b/onnxruntime/core/providers/webgpu/webgpu_context.h
index 80c8c64ce72b6..1a752a93a7116 100644
--- a/onnxruntime/core/providers/webgpu/webgpu_context.h
+++ b/onnxruntime/core/providers/webgpu/webgpu_context.h
@@ -6,7 +6,7 @@
 #include <memory>
 #include <mutex>
 
-#include <webgpu/webgpu_cpp.h>
+#include "core/providers/webgpu/webgpu_external_header.h"
 
 #include "core/common/common.h"
 #include "core/framework/library_handles.h"
diff --git a/onnxruntime/core/providers/webgpu/webgpu_external_header.h b/onnxruntime/core/providers/webgpu/webgpu_external_header.h
new file mode 100644
index 0000000000000..485fa729f1d9f
--- /dev/null
+++ b/onnxruntime/core/providers/webgpu/webgpu_external_header.h
@@ -0,0 +1,15 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+#pragma once
+
+#if defined(__GNUC__)
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wstrict-aliasing"
+#endif
+
+#include <webgpu/webgpu_cpp.h>
+
+#if defined(__GNUC__)
+#pragma GCC diagnostic pop
+#endif