diff --git a/js/common/lib/env.ts b/js/common/lib/env.ts
index 76575ef7b9..0cded7e5ed 100644
--- a/js/common/lib/env.ts
+++ b/js/common/lib/env.ts
@@ -92,11 +92,48 @@ export declare namespace Env {
     async?: boolean;
   }
 
+  export interface WebGpuProfilingDataV1TensorMetadata {
+    dims: readonly number[];
+    dataType: string;
+  }
+  export interface WebGpuProfilingDataV1 {
+    version: 1;
+    inputsMetadata: readonly WebGpuProfilingDataV1TensorMetadata[];
+    outputsMetadata: readonly WebGpuProfilingDataV1TensorMetadata[];
+    kernelId: number;
+    kernelType: string;
+    kernelName: string;
+    startTime: number;
+    endTime: number;
+  }
+
+  export type WebGpuProfilingData = WebGpuProfilingDataV1;
+
   export interface WebGpuFlags {
     /**
      * Set or get the profiling mode.
+     *
+     * @deprecated Use `env.webgpu.profiling.mode` instead. If `env.webgpu.profiling.mode` is set, this property will be
+     * ignored.
      */
     profilingMode?: 'off'|'default';
+    /**
+     * Set or get the profiling configuration.
+     */
+    profiling?: {
+      /**
+       * Set or get the profiling mode.
+       *
+       * @defaultValue `'off'`
+       */
+      mode?: 'off'|'default';
+
+      /**
+       * Set or get a callback function when a profiling data is received. If not set, the profiling data will be
+       * printed to console.
+       */
+      ondata?: (data: WebGpuProfilingData) => void;
+    };
     /**
      * Get the device for WebGPU.
      *
diff --git a/js/web/lib/wasm/jsep/backend-webgpu.ts b/js/web/lib/wasm/jsep/backend-webgpu.ts
index bb86f147c9..4f4a06c37a 100644
--- a/js/web/lib/wasm/jsep/backend-webgpu.ts
+++ b/js/web/lib/wasm/jsep/backend-webgpu.ts
@@ -254,11 +254,9 @@ export class WebGpuBackend {
   }
 
   isQueryEnabled(): boolean {
-    if (this.device.features.has('timestamp-query') && this.env.webgpu.profilingMode === 'default') {
-      return true;
-    } else {
-      return false;
-    }
+    return this.device.features.has('timestamp-query') &&
+        (this.env.webgpu.profiling?.mode === 'default' ||
+         (!this.env.webgpu.profiling?.mode && this.env.webgpu.profilingMode === 'default'));
   }
 
   /**
diff --git a/js/web/lib/wasm/jsep/init.ts b/js/web/lib/wasm/jsep/init.ts
index d66357e729..e6db631c44 100644
--- a/js/web/lib/wasm/jsep/init.ts
+++ b/js/web/lib/wasm/jsep/init.ts
@@ -175,8 +175,7 @@ export const init = async(module: OrtWasmModule, env: Env): Promise<void> => {
         // jsepCreateKernel
         (name: string, kernel: number, attribute: unknown) => backend.createKernel(
             name, kernel, attribute,
-            env.debug || env.webgpu.profilingMode === 'default' ? module.UTF8ToString(module._JsepGetNodeName(kernel)) :
-                                                                  `${kernel}`),
+            env.debug || backend.isQueryEnabled() ? module.UTF8ToString(module._JsepGetNodeName(kernel)) : `${kernel}`),
 
         // jsepReleaseKernel
         (kernel: number) => backend.releaseKernel(kernel),
diff --git a/js/web/lib/wasm/jsep/webgpu/program-manager.ts b/js/web/lib/wasm/jsep/webgpu/program-manager.ts
index 9d50a0a6fb..adf0b1b296 100644
--- a/js/web/lib/wasm/jsep/webgpu/program-manager.ts
+++ b/js/web/lib/wasm/jsep/webgpu/program-manager.ts
@@ -75,12 +75,11 @@ export class ProgramManager {
 
       const kernelId = this.backend.currentKernelId!;
       const kernelInfo = this.backend.kernels.get(kernelId)!;
-      const kernelName = `[${kernelInfo[0]}] ${kernelInfo[1]}`;
 
       void syncData.buffer.mapAsync(GPUMapMode.READ).then(() => {
         const mappedData = new BigUint64Array(syncData.buffer.getMappedRange());
-        const startTimeU64 = mappedData[0];
-        const endTimeU64 = mappedData[1];
+        const [startTimeU64, endTimeU64] = mappedData;
+        const [kernelType, kernelName] = kernelInfo;
 
         syncData.buffer.unmap();
 
@@ -96,17 +95,33 @@ export class ProgramManager {
         }
 
         this.backend.gpuDataManager.release(syncData.id);
-        let inputShapes = '';
-        inputTensorViews.forEach((value, i) => {
-          inputShapes += `input[${i}]: [${value.dims}] | ${tensorDataTypeEnumToString(value.dataType)}, `;
-        });
-        let outputShapes = '';
-        outputTensorViews.forEach((value, i) => {
-          outputShapes += `output[${i}]: [${value.dims}] | ${tensorDataTypeEnumToString(value.dataType)}, `;
-        });
-        // eslint-disable-next-line no-console
-        console.log(`[profiling] kernel "${kernelId}|${kernelName}|${buildArtifact.programInfo.name}" ${inputShapes}${
-            outputShapes}execution time: ${endTime - startTime} ns`);
+        if (this.backend.env.webgpu.profiling?.ondata) {
+          this.backend.env.webgpu.profiling.ondata({
+            version: 1,
+            inputsMetadata: inputTensorViews.map(
+                value => ({dims: value.dims, dataType: tensorDataTypeEnumToString(value.dataType)})),
+            outputsMetadata: outputTensorViews.map(
+                value => ({dims: value.dims, dataType: tensorDataTypeEnumToString(value.dataType)})),
+            kernelId,
+            kernelType,
+            kernelName,
+            startTime,
+            endTime,
+          });
+        } else {
+          // if no callback is provided, print the profiling message to console
+          let inputShapes = '';
+          inputTensorViews.forEach((value, i) => {
+            inputShapes += `input[${i}]: [${value.dims}] | ${tensorDataTypeEnumToString(value.dataType)}, `;
+          });
+          let outputShapes = '';
+          inputTensorViews.forEach((value, i) => {
+            outputShapes += `output[${i}]: [${value.dims}] | ${tensorDataTypeEnumToString(value.dataType)}, `;
+          });
+          // eslint-disable-next-line no-console
+          console.log(`[profiling] kernel "${kernelId}|${kernelName}|${buildArtifact.programInfo.name}" ${inputShapes}${
+              outputShapes}execution time: ${endTime - startTime} ns`);
+        }
       });
     }
 
diff --git a/js/web/test/test-main.ts b/js/web/test/test-main.ts
index 24ab0694b3..9bd0ec1425 100644
--- a/js/web/test/test-main.ts
+++ b/js/web/test/test-main.ts
@@ -56,7 +56,7 @@ if (options.globalEnvFlags) {
     ort.env.wasm.initTimeout = flags.wasm.initTimeout;
   }
   if (flags.webgpu?.profilingMode !== undefined) {
-    ort.env.webgpu.profilingMode = flags.webgpu.profilingMode;
+    ort.env.webgpu.profiling = {mode: flags.webgpu.profilingMode};
   }
   if (flags.webgpu?.validateInputContent !== undefined) {
     ort.env.webgpu.validateInputContent = flags.webgpu.validateInputContent;