diff --git a/web/lib/build-def.d.ts b/web/lib/build-def.d.ts
index b3868871a4753..2c9cd88a375bd 100644
--- a/web/lib/build-def.d.ts
+++ b/web/lib/build-def.d.ts
@@ -21,10 +21,6 @@ interface BuildDefinitions {
   /**
    * defines whether to disable the whole WebNN backend in the build.
    */
-  readonly DISABLE_WEBNN: boolean;
-  /**
-   * defines whether to disable the whole WebAssembly backend in the build.
-   */
   readonly DISABLE_WASM: boolean;
   /**
    * defines whether to disable proxy feature in WebAssembly backend in the build.
diff --git a/web/lib/index.ts b/web/lib/index.ts
index baf45e74addea..b212c0f49df3b 100644
--- a/web/lib/index.ts
+++ b/web/lib/index.ts
@@ -23,12 +23,10 @@ if (!BUILD_DEFS.DISABLE_WASM) {
                                                     require('./backend-wasm-training').wasmBackend;
   if (!BUILD_DEFS.DISABLE_WEBGPU) {
     registerBackend('webgpu', wasmBackend, 5);
+    registerBackend('webnn', wasmBackend, 5);
   }
   registerBackend('cpu', wasmBackend, 10);
   registerBackend('wasm', wasmBackend, 10);
-  if (!BUILD_DEFS.DISABLE_WEBNN) {
-    registerBackend('webnn', wasmBackend, 9);
-  }
 }
 
 Object.defineProperty(env.versions, 'web', {value: version, enumerable: true});
diff --git a/web/lib/wasm/binding/ort-wasm.d.ts b/web/lib/wasm/binding/ort-wasm.d.ts
index 68054210e79a7..24d7062c85fcb 100644
--- a/web/lib/wasm/binding/ort-wasm.d.ts
+++ b/web/lib/wasm/binding/ort-wasm.d.ts
@@ -31,7 +31,7 @@ export interface OrtWasmModule extends EmscriptenModule {
 
   _OrtGetLastError(errorCodeOffset: number, errorMessageOffset: number): void;
 
-  _OrtCreateSession(dataOffset: number, dataLength: number, sessionOptionsHandle: number): number;
+  _OrtCreateSession(dataOffset: number, dataLength: number, sessionOptionsHandle: number): Promise<number>;
   _OrtReleaseSession(sessionHandle: number): void;
   _OrtGetInputOutputCount(sessionHandle: number, inputCountOffset: number, outputCountOffset: number): number;
   _OrtGetInputName(sessionHandle: number, index: number): number;
diff --git a/web/lib/wasm/wasm-core-impl.ts b/web/lib/wasm/wasm-core-impl.ts
index 8768643fa7257..046336dc9cac0 100644
--- a/web/lib/wasm/wasm-core-impl.ts
+++ b/web/lib/wasm/wasm-core-impl.ts
@@ -84,7 +84,7 @@ export const initRuntime = async(env: Env): Promise<void> => {
  * @param epName
  */
 export const initEp = async(env: Env, epName: string): Promise<void> => {
-  if (!BUILD_DEFS.DISABLE_WEBGPU && epName === 'webgpu') {
+  if (!BUILD_DEFS.DISABLE_WEBGPU && (epName === 'webgpu' || epName === 'webnn')) {
     // perform WebGPU availability check
     if (typeof navigator === 'undefined' || !navigator.gpu) {
       throw new Error('WebGPU is not supported in current environment');
@@ -228,7 +228,7 @@ export const createSession = async(
       await Promise.all(loadingPromises);
     }
 
-    sessionHandle = wasm._OrtCreateSession(modelDataOffset, modelDataLength, sessionOptionsHandle);
+    sessionHandle = await wasm._OrtCreateSession(modelDataOffset, modelDataLength, sessionOptionsHandle);
     if (sessionHandle === 0) {
       checkLastError('Can\'t create a session.');
     }
diff --git a/web/script/build.ts b/web/script/build.ts
index ea0c122cb51de..d3652f3820357 100644
--- a/web/script/build.ts
+++ b/web/script/build.ts
@@ -44,7 +44,6 @@ const SOURCE_ROOT_FOLDER = path.join(__dirname, '../..');  // <ORT_ROOT>/js/
 const DEFAULT_DEFINE = {
   'BUILD_DEFS.DISABLE_WEBGL': 'false',
   'BUILD_DEFS.DISABLE_WEBGPU': 'false',
-  'BUILD_DEFS.DISABLE_WEBNN': 'false',
   'BUILD_DEFS.DISABLE_WASM': 'false',
   'BUILD_DEFS.DISABLE_WASM_PROXY': 'false',
   'BUILD_DEFS.DISABLE_WASM_THREAD': 'false',
@@ -364,7 +363,6 @@ async function main() {
         ...DEFAULT_DEFINE,
         'BUILD_DEFS.DISABLE_WEBGPU': 'true',
         'BUILD_DEFS.DISABLE_WEBGL': 'true',
-        'BUILD_DEFS.DISABLE_WEBNN': 'true',
         'BUILD_DEFS.DISABLE_WASM_PROXY': 'true',
         'BUILD_DEFS.DISABLE_WASM_THREAD': 'true',
       },
@@ -397,7 +395,7 @@ async function main() {
     // ort.webgpu[.min].js
     await addAllWebBuildTasks({
       outputBundleName: 'ort.webgpu',
-      define: {...DEFAULT_DEFINE, 'BUILD_DEFS.DISABLE_WEBGL': 'true', 'BUILD_DEFS.DISABLE_WEBNN': 'true'},
+      define: {...DEFAULT_DEFINE, 'BUILD_DEFS.DISABLE_WEBGL': 'true'},
     });
     // ort.wasm[.min].js
     await addAllWebBuildTasks({
@@ -411,7 +409,6 @@ async function main() {
         ...DEFAULT_DEFINE,
         'BUILD_DEFS.DISABLE_WEBGPU': 'true',
         'BUILD_DEFS.DISABLE_WASM': 'true',
-        'BUILD_DEFS.DISABLE_WEBNN': 'true',
       },
     });
     // ort.wasm-core[.min].js
@@ -421,7 +418,6 @@ async function main() {
         ...DEFAULT_DEFINE,
         'BUILD_DEFS.DISABLE_WEBGPU': 'true',
         'BUILD_DEFS.DISABLE_WEBGL': 'true',
-        'BUILD_DEFS.DISABLE_WEBNN': 'true',
         'BUILD_DEFS.DISABLE_WASM_PROXY': 'true',
         'BUILD_DEFS.DISABLE_WASM_THREAD': 'true',
       },
@@ -434,7 +430,6 @@ async function main() {
         'BUILD_DEFS.DISABLE_TRAINING': 'false',
         'BUILD_DEFS.DISABLE_WEBGPU': 'true',
         'BUILD_DEFS.DISABLE_WEBGL': 'true',
-        'BUILD_DEFS.DISABLE_WEBNN': 'true',
       },
     });
   }
diff --git a/web/script/test-runner-cli-args.ts b/web/script/test-runner-cli-args.ts
index 8f6c5f6f04122..ed4dd76a6e315 100644
--- a/web/script/test-runner-cli-args.ts
+++ b/web/script/test-runner-cli-args.ts
@@ -396,10 +396,6 @@ export function parseTestRunnerCliArgs(cmdlineArgs: string[]): TestRunnerCliArgs
 
   const globalEnvFlags = parseGlobalEnvFlags(args);
 
-  if (backend.includes('webnn') && !globalEnvFlags.wasm!.proxy) {
-    throw new Error('Backend webnn requires flag "wasm-enable-proxy" to be set to true.');
-  }
-
   // Options:
   // --log-verbose=<...>
   // --log-info=<...>