diff --git a/js/web/lib/wasm/binding/ort-wasm.d.ts b/js/web/lib/wasm/binding/ort-wasm.d.ts
index 9d4d5875310b7..68054210e79a7 100644
--- a/js/web/lib/wasm/binding/ort-wasm.d.ts
+++ b/js/web/lib/wasm/binding/ort-wasm.d.ts
@@ -182,6 +182,10 @@ export interface OrtWasmModule extends EmscriptenModule {
   jsepCreateDownloader:
       (gpuBuffer: GPUBuffer, size: number,
        type: Tensor.GpuBufferDataTypes) => () => Promise<Tensor.DataTypeMap[Tensor.GpuBufferDataTypes]>;
+  /**
+   *  [exported from js_internal_api.js] Called when InferenceSession.run started.
+   */
+  jsepOnRunStart: () => void;
   // #endregion
 }
 
diff --git a/js/web/lib/wasm/jsep/backend-webgpu.ts b/js/web/lib/wasm/jsep/backend-webgpu.ts
index 2956ec1cad4da..afef7042a4280 100644
--- a/js/web/lib/wasm/jsep/backend-webgpu.ts
+++ b/js/web/lib/wasm/jsep/backend-webgpu.ts
@@ -208,7 +208,7 @@ export class WebGpuBackend {
 
     Object.defineProperty(this.env.webgpu, 'device', {value: this.device});
 
-    // init queryType, which is necessary for createKernel
+    // init queryType, which is necessary for InferenceSession.create
     this.setQueryType();
   }
 
@@ -223,8 +223,6 @@ export class WebGpuBackend {
     if (!this.commandEncoder) {
       this.commandEncoder = this.device.createCommandEncoder();
 
-      // refresh queryType, as sometimes we only need to enable query for a specific run
-      this.setQueryType();
       if (this.queryType !== 'none' && typeof this.querySet === 'undefined') {
         this.querySet = this.device.createQuerySet({
           type: 'timestamp',
@@ -639,6 +637,7 @@ export class WebGpuBackend {
       return createView(data.buffer, type);
     };
   }
+  // #endregion
   writeTimestamp(index: number): void {
     if (this.queryType !== 'inside-passes') {
       return;
@@ -657,5 +656,7 @@ export class WebGpuBackend {
       }
     }
   }
-  // #endregion
+  onRunStart(): void {
+    this.setQueryType();
+  }
 }
diff --git a/js/web/lib/wasm/wasm-core-impl.ts b/js/web/lib/wasm/wasm-core-impl.ts
index 5821fac3c468f..8768643fa7257 100644
--- a/js/web/lib/wasm/wasm-core-impl.ts
+++ b/js/web/lib/wasm/wasm-core-impl.ts
@@ -488,8 +488,8 @@ export const run = async(
       }
     }
 
+    wasm.jsepOnRunStart?.();
     let errorCode: number;
-
     if (!BUILD_DEFS.DISABLE_WEBGPU && ioBindingState) {
       errorCode = await wasm._OrtRunWithBinding(
           sessionHandle, ioBindingState.handle, outputCount, outputValuesOffset, runOptionsHandle);
diff --git a/onnxruntime/wasm/js_internal_api.js b/onnxruntime/wasm/js_internal_api.js
index 25ece9c700d5d..7c70515e73eab 100644
--- a/onnxruntime/wasm/js_internal_api.js
+++ b/onnxruntime/wasm/js_internal_api.js
@@ -186,4 +186,7 @@ Module['jsepInit'] = (backend, alloc, free, copy, copyAsync, createKernel, relea
   Module['jsepCreateDownloader'] = (gpuBuffer, size, type) => {
     return backend['createDownloader'](gpuBuffer, size, type);
   };
+  Module['jsepOnRunStart'] = () => {
+    return backend['onRunStart']();
+  };
 };