diff --git a/js/web/lib/onnxjs/backends/webgpu/gpu-data-manager.ts b/js/web/lib/onnxjs/backends/webgpu/gpu-data-manager.ts
index c9f767bdc191a..d7eb843a031db 100644
--- a/js/web/lib/onnxjs/backends/webgpu/gpu-data-manager.ts
+++ b/js/web/lib/onnxjs/backends/webgpu/gpu-data-manager.ts
@@ -42,6 +42,11 @@ interface DownloadCacheValue {
   data: Promise<ArrayBufferLike>;
 }
 
+/**
+ * normalize the buffer size so that it fits the 128-bits (16 bytes) alignment.
+ */
+const calcNormalizedBufferSize = (size: number) => Math.ceil(size / 16) * 16;
+
 class GpuDataManagerImpl implements GpuDataManager {
   // GPU Data ID => GPU Data ( storage buffer )
   storageCache: Map<GpuDataId, StorageCacheValue>;
@@ -62,10 +67,10 @@ class GpuDataManagerImpl implements GpuDataManager {
     const srcArrayBuffer = data.buffer;
     const srcOffset = data.byteOffset;
     const srcLength = data.byteLength;
+    const size = calcNormalizedBufferSize(srcLength);
 
     // create gpu buffer
-    const gpuBuffer =
-        this.device.createBuffer({mappedAtCreation: true, size: srcLength, usage: GPUBufferUsage.STORAGE});
+    const gpuBuffer = this.device.createBuffer({mappedAtCreation: true, size, usage: GPUBufferUsage.STORAGE});
 
     // copy (upload) data
     const arrayBuffer = gpuBuffer.getMappedRange();
@@ -89,11 +94,12 @@ class GpuDataManagerImpl implements GpuDataManager {
 
     const elemCount = ShapeUtil.size(dims);
     const bufferLength = sizeof(type) * elemCount;
+    const size = calcNormalizedBufferSize(bufferLength);
 
     // create gpu buffer
     const gpuBuffer =
         // eslint-disable-next-line no-bitwise
-        this.device.createBuffer({size: bufferLength, usage: GPUBufferUsage.STORAGE | GPUBufferUsage.COPY_SRC});
+        this.device.createBuffer({size, usage: GPUBufferUsage.STORAGE | GPUBufferUsage.COPY_SRC});
 
     const gpuData = {id: Guid.create(), type: GpuDataType.default, buffer: gpuBuffer};
     this.storageCache.set(gpuData.id, {gpuData, size: bufferLength});