diff --git a/js/web/lib/wasm/binding/ort-wasm.d.ts b/js/web/lib/wasm/binding/ort-wasm.d.ts
index d04578ca69..06fcbf6344 100644
--- a/js/web/lib/wasm/binding/ort-wasm.d.ts
+++ b/js/web/lib/wasm/binding/ort-wasm.d.ts
@@ -78,7 +78,7 @@ export interface OrtWasmModule extends EmscriptenModule {
   _JsepGetNodeName(kernel: number): number;
 
   jsepOnRunStart?(sessionId: number): void;
-  jsepOnRunEnd?(sessionId: number): void;
+  jsepOnRunEnd?(sessionId: number): Promise<void>;
   jsepRunPromise?: Promise<number>;
   // #endregion
 }
diff --git a/js/web/lib/wasm/wasm-core-impl.ts b/js/web/lib/wasm/wasm-core-impl.ts
index 9dc55b0d12..fcca82ab2a 100644
--- a/js/web/lib/wasm/wasm-core-impl.ts
+++ b/js/web/lib/wasm/wasm-core-impl.ts
@@ -258,6 +258,7 @@ export const run = async(
         wasm.HEAPU32[outputNamesIndex++] = outputNamesUTF8Encoded[outputIndices[i]];
       }
 
+      // jsepOnRunStart is only available when JSEP is enabled.
       wasm.jsepOnRunStart?.(sessionId);
 
       // support RunOptions
@@ -265,13 +266,28 @@ export const run = async(
           sessionHandle, inputNamesOffset, inputValuesOffset, inputCount, outputNamesOffset, outputCount,
           outputValuesOffset, runOptionsHandle);
 
-      wasm.jsepOnRunEnd?.(sessionId);
-
       const runPromise = wasm.jsepRunPromise;
-      if (runPromise && typeof runPromise.then !== 'undefined') {
+      if (runPromise) {
+        // jsepRunPromise is a Promise object. It is only available when JSEP is enabled.
+        //
+        // OrtRun() is a synchrnous call, but it internally calls async functions. Emscripten's ASYNCIFY allows it to
+        // work in this way. However, OrtRun() does not return a promise, so when code reaches here, it is earlier than
+        // the async functions are finished.
+        //
+        // To make it work, we created a Promise and resolve the promise when the C++ code actually reaches the end of
+        // OrtRun(). If the promise exists, we need to await for the promise to be resolved.
         errorCode = await runPromise;
       }
 
+      const jsepOnRunEnd = wasm.jsepOnRunEnd;
+      if (jsepOnRunEnd) {
+        // jsepOnRunEnd is only available when JSEP is enabled.
+        //
+        // it returns a promise, which is resolved or rejected when the following async functions are finished:
+        // - collecting GPU validation errors.
+        await jsepOnRunEnd(sessionId);
+      }
+
       const output: SerializableTensor[] = [];
 
       if (errorCode !== 0) {
diff --git a/onnxruntime/wasm/js_internal_api.js b/onnxruntime/wasm/js_internal_api.js
index c7bc0e39fc..15d393f4ce 100644
--- a/onnxruntime/wasm/js_internal_api.js
+++ b/onnxruntime/wasm/js_internal_api.js
@@ -37,20 +37,17 @@ Module['jsepInit'] = (backend, alloc, free, copy, copyAsync, createKernel, relea
     const errorPromises = Module.jsepSessionState.errors;
     Module.jsepSessionState = null;
 
-    if (errorPromises.length > 0) {
-      const runPromise = Module['jsepRunPromise'];
-      Module['jsepRunPromise'] = new Promise((resolve, reject) => {
-        Promise.all(errorPromises).then(errors => {
-          errors = errors.filter(e => e);
-          if (errors.length > 0) {
-            reject(new Error(errors.join('\n')));
-          } else {
-            resolve(runPromise);
-          }
-        }, reason => {
-          reject(reason);
-        });
+    return errorPromises.length === 0 ? Promise.resolve() : new Promise((resolve, reject) => {
+      Promise.all(errorPromises).then(errors => {
+        errors = errors.filter(e => e);
+        if (errors.length > 0) {
+          reject(new Error(errors.join('\n')));
+        } else {
+          resolve();
+        }
+      }, reason => {
+        reject(reason);
       });
-    }
+    });
   };
 };