diff --git a/js/common/lib/inference-session.ts b/js/common/lib/inference-session.ts
index 8c1e69a68ca7e..c7760692eed00 100644
--- a/js/common/lib/inference-session.ts
+++ b/js/common/lib/inference-session.ts
@@ -241,6 +241,7 @@ export declare namespace InferenceSession {
   export interface WebNNExecutionProviderOption extends ExecutionProviderOption {
     readonly name: 'webnn';
     deviceType?: 'cpu'|'gpu';
+    numThreads?: number;
     powerPreference?: 'default'|'low-power'|'high-performance';
   }
   export interface CoreMLExecutionProviderOption extends ExecutionProviderOption {
diff --git a/js/web/lib/wasm/session-options.ts b/js/web/lib/wasm/session-options.ts
index 02ff229cc4954..45ea48a2df209 100644
--- a/js/web/lib/wasm/session-options.ts
+++ b/js/web/lib/wasm/session-options.ts
@@ -75,6 +75,19 @@ const setExecutionProviders =
                   checkLastError(`Can't set a session config entry: 'deviceType' - ${webnnOptions.deviceType}.`);
                 }
               }
+              if (webnnOptions?.numThreads) {
+                let numThreads = webnnOptions.numThreads;
+                // Just ignore invalid webnnOptions.numThreads.
+                if (typeof numThreads != 'number' || !Number.isInteger(numThreads) || numThreads < 0) {
+                  numThreads = 0;
+                }
+                const keyDataOffset = allocWasmString('numThreads', allocs);
+                const valueDataOffset = allocWasmString(numThreads.toString(), allocs);
+                if (getInstance()._OrtAddSessionConfigEntry(sessionOptionsHandle, keyDataOffset, valueDataOffset) !==
+                    0) {
+                  checkLastError(`Can't set a session config entry: 'numThreads' - ${webnnOptions.numThreads}.`);
+                }
+              }
               if (webnnOptions?.powerPreference) {
                 const keyDataOffset = allocWasmString('powerPreference', allocs);
                 const valueDataOffset = allocWasmString(webnnOptions.powerPreference, allocs);
diff --git a/onnxruntime/core/providers/webnn/webnn_execution_provider.cc b/onnxruntime/core/providers/webnn/webnn_execution_provider.cc
index 02a3d16b5b64f..4da54aaad3a33 100644
--- a/onnxruntime/core/providers/webnn/webnn_execution_provider.cc
+++ b/onnxruntime/core/providers/webnn/webnn_execution_provider.cc
@@ -17,8 +17,8 @@
 
 namespace onnxruntime {
 
-WebNNExecutionProvider::WebNNExecutionProvider(
-    const std::string& webnn_device_flags, const std::string& webnn_power_flags)
+WebNNExecutionProvider::WebNNExecutionProvider(const std::string& webnn_device_flags,
+                                               const std::string& webnn_threads_number, const std::string& webnn_power_flags)
     : IExecutionProvider{onnxruntime::kWebNNExecutionProvider, true} {
   // Create WebNN context and graph builder.
   const emscripten::val ml = emscripten::val::global("navigator")["ml"];
@@ -31,6 +31,10 @@ WebNNExecutionProvider::WebNNExecutionProvider(
   if (webnn_device_flags.compare("cpu") == 0) {
     preferred_layout_ = DataLayout::NHWC;
     wnn_device_type_ = webnn::WebnnDeviceType::CPU;
+    // Set "numThreads" if it's not default 0.
+    if (webnn_threads_number.compare("0") != 0) {
+      context_options.set("numThreads", stoi(webnn_threads_number));
+    }
   } else {
     preferred_layout_ = DataLayout::NCHW;
     wnn_device_type_ = webnn::WebnnDeviceType::GPU;
diff --git a/onnxruntime/core/providers/webnn/webnn_execution_provider.h b/onnxruntime/core/providers/webnn/webnn_execution_provider.h
index f8d9a1c33f6c8..13a475327dc0c 100644
--- a/onnxruntime/core/providers/webnn/webnn_execution_provider.h
+++ b/onnxruntime/core/providers/webnn/webnn_execution_provider.h
@@ -18,7 +18,8 @@ class Model;
 
 class WebNNExecutionProvider : public IExecutionProvider {
  public:
-  WebNNExecutionProvider(const std::string& webnn_device_flags, const std::string& webnn_power_flags);
+  WebNNExecutionProvider(const std::string& webnn_device_flags, const std::string& webnn_threads_number,
+                         const std::string& webnn_power_flags);
   virtual ~WebNNExecutionProvider();
 
   std::vector<std::unique_ptr<ComputeCapability>>
diff --git a/onnxruntime/core/providers/webnn/webnn_provider_factory.cc b/onnxruntime/core/providers/webnn/webnn_provider_factory.cc
index 4d6b04c8e76d8..11acec8b1f354 100644
--- a/onnxruntime/core/providers/webnn/webnn_provider_factory.cc
+++ b/onnxruntime/core/providers/webnn/webnn_provider_factory.cc
@@ -10,23 +10,26 @@ using namespace onnxruntime;
 
 namespace onnxruntime {
 struct WebNNProviderFactory : IExecutionProviderFactory {
-  WebNNProviderFactory(const std::string& webnn_device_flags, const std::string& webnn_power_flags)
-      : webnn_device_flags_(webnn_device_flags), webnn_power_flags_(webnn_power_flags) {}
+  WebNNProviderFactory(const std::string& webnn_device_flags, const std::string& webnn_threads_number,
+                       const std::string& webnn_power_flags)
+      : webnn_device_flags_(webnn_device_flags), webnn_threads_number_(webnn_threads_number), webnn_power_flags_(webnn_power_flags) {}
   ~WebNNProviderFactory() override {}
 
   std::unique_ptr<IExecutionProvider> CreateProvider() override;
 
   std::string webnn_device_flags_;
+  std::string webnn_threads_number_;
   std::string webnn_power_flags_;
 };
 
 std::unique_ptr<IExecutionProvider> WebNNProviderFactory::CreateProvider() {
-  return std::make_unique<WebNNExecutionProvider>(webnn_device_flags_, webnn_power_flags_);
+  return std::make_unique<WebNNExecutionProvider>(webnn_device_flags_, webnn_threads_number_, webnn_power_flags_);
 }
 
 std::shared_ptr<IExecutionProviderFactory> WebNNProviderFactoryCreator::Create(
     const ProviderOptions& provider_options) {
   return std::make_shared<onnxruntime::WebNNProviderFactory>(provider_options.at("deviceType"),
+                                                             provider_options.at("numThreads"),
                                                              provider_options.at("powerPreference"));
 }
 
diff --git a/onnxruntime/core/session/provider_registration.cc b/onnxruntime/core/session/provider_registration.cc
index 4649ac35c3647..cb51a0c460d9a 100644
--- a/onnxruntime/core/session/provider_registration.cc
+++ b/onnxruntime/core/session/provider_registration.cc
@@ -104,8 +104,10 @@ ORT_API_STATUS_IMPL(OrtApis::SessionOptionsAppendExecutionProvider,
   } else if (strcmp(provider_name, "WEBNN") == 0) {
 #if defined(USE_WEBNN)
     std::string deviceType = options->value.config_options.GetConfigOrDefault("deviceType", "cpu");
+    std::string numThreads = options->value.config_options.GetConfigOrDefault("numThreads", "0");
     std::string powerPreference = options->value.config_options.GetConfigOrDefault("powerPreference", "default");
     provider_options["deviceType"] = deviceType;
+    provider_options["numThreads"] = numThreads;
     provider_options["powerPreference"] = powerPreference;
     options->provider_factories.push_back(WebNNProviderFactoryCreator::Create(provider_options));
 #else