diff --git a/.gitmodules b/.gitmodules
index a48c4062a90fe..37455d1bb64c2 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -7,4 +7,4 @@
 [submodule "cmake/external/emsdk"]
 	path = cmake/external/emsdk
 	url = https://github.com/emscripten-core/emsdk.git
-	branch = 4.0.11
+	branch = 4.0.21
diff --git a/cmake/external/emsdk b/cmake/external/emsdk
index d49219d03a41c..b2436aafa7351 160000
--- a/cmake/external/emsdk
+++ b/cmake/external/emsdk
@@ -1 +1 @@
-Subproject commit d49219d03a41cd12f95a33ba84273c20d41fd350
+Subproject commit b2436aafa7351ee1b581f15841f1b45ed716a279
diff --git a/cmake/onnxruntime_providers_webgpu.cmake b/cmake/onnxruntime_providers_webgpu.cmake
index 62f594d194543..f382f70ffedb0 100644
--- a/cmake/onnxruntime_providers_webgpu.cmake
+++ b/cmake/onnxruntime_providers_webgpu.cmake
@@ -58,6 +58,20 @@
     # WebAssembly/JavaScript code for WebGPU support.
     target_link_libraries(onnxruntime_providers_webgpu PUBLIC emdawnwebgpu_cpp)
 
+    # Dawn's emdawnwebgpu_cpp target has a bug: it lists ${DAWN_INCLUDE_DIR}/webgpu/webgpu_enum_class_bitmasks.h
+    # in INTERFACE_SOURCES but doesn't add ${DAWN_INCLUDE_DIR} to INTERFACE_INCLUDE_DIRECTORIES.
+    # In emsdk 4.0.11, this was masked because Emscripten bundled its own copy of the WebGPU headers.
+    # In emsdk 4.0.21+, Emscripten removed the bundled WebGPU headers, exposing this bug.
+    # We need to manually add the Dawn include directory to find webgpu_enum_class_bitmasks.h.
+    #
+    # IMPORTANT: We must also add the generated emdawnwebgpu include directory BEFORE the Dawn source
+    # include directory, because ${dawn_SOURCE_DIR}/include/webgpu/webgpu_cpp.h is a stub that redirects
+    # to dawn/webgpu_cpp.h (native Dawn), but we need the generated Emscripten-specific webgpu_cpp.h.
+    target_include_directories(onnxruntime_providers_webgpu PRIVATE
+        "${dawn_BINARY_DIR}/gen/src/emdawnwebgpu/include"
+        "${dawn_SOURCE_DIR}/include"
+    )
+
     if (onnxruntime_ENABLE_WEBASSEMBLY_JSPI)
       target_link_options(onnxruntime_providers_webgpu PUBLIC
         "SHELL:-s JSPI=1"
diff --git a/tools/ci_build/build_args.py b/tools/ci_build/build_args.py
index 6763973406294..8f79598b2381c 100644
--- a/tools/ci_build/build_args.py
+++ b/tools/ci_build/build_args.py
@@ -359,7 +359,7 @@ def add_webassembly_args(parser: argparse.ArgumentParser) -> None:
     """Adds arguments for WebAssembly (WASM) platform builds."""
     parser.add_argument("--build_wasm", action="store_true", help="Build for WebAssembly.")
     parser.add_argument("--build_wasm_static_lib", action="store_true", help="Build WebAssembly static library.")
-    parser.add_argument("--emsdk_version", default="4.0.11", help="Specify version of emsdk.")
+    parser.add_argument("--emsdk_version", default="4.0.21", help="Specify version of emsdk.")
     parser.add_argument(
         "--enable_wasm_jspi", action="store_true", help="Enable WebAssembly JavaScript Promise Integration."
     )
diff --git a/tools/ci_build/github/azure-pipelines/templates/linux-wasm-ci.yml b/tools/ci_build/github/azure-pipelines/templates/linux-wasm-ci.yml
index 249c866b88df4..6cb16313ef309 100644
--- a/tools/ci_build/github/azure-pipelines/templates/linux-wasm-ci.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/linux-wasm-ci.yml
@@ -96,15 +96,15 @@ jobs:
     - script: |
         set -ex
         cd '$(Build.SourcesDirectory)/cmake/external/emsdk'
-        ./emsdk install 4.0.11 ccache-git-emscripten-64bit
-        ./emsdk activate 4.0.11 ccache-git-emscripten-64bit
+        ./emsdk install 4.0.21 ccache-git-emscripten-64bit
+        ./emsdk activate 4.0.21 ccache-git-emscripten-64bit
       displayName: 'emsdk install and activate ccache for emscripten'
   - ${{if eq(parameters.WithCache, false)}}:
     - script: |
         set -ex
         cd '$(Build.SourcesDirectory)/cmake/external/emsdk'
-        ./emsdk install 4.0.11
-        ./emsdk activate 4.0.11
+        ./emsdk install 4.0.21
+        ./emsdk activate 4.0.21
       displayName: 'emsdk install and activate ccache for emscripten'
 
   - template: build-linux-wasm-step.yml
diff --git a/tools/python/util/vcpkg_helpers.py b/tools/python/util/vcpkg_helpers.py
index 415aeaf22211d..182d757907ab2 100644
--- a/tools/python/util/vcpkg_helpers.py
+++ b/tools/python/util/vcpkg_helpers.py
@@ -24,9 +24,24 @@ def add_port_configs(f, has_exception: bool, is_emscripten: bool, enable_minimal
     list(APPEND VCPKG_CMAKE_CONFIGURE_OPTIONS
         "-DBENCHMARK_ENABLE_WERROR=OFF"
     )
-endif()
 """
     )
+    if is_emscripten:
+        # workaround for https://github.com/google/benchmark/issues/2057
+        f.write(
+            r"""
+    string(APPEND VCPKG_C_FLAGS
+        " -Wno-c2y-extensions"
+    )
+    string(APPEND VCPKG_CXX_FLAGS
+        " -Wno-c2y-extensions"
+    )
+"""
+        )
+    f.write(r"""
+endif()  # benchmark
+""")
+
     f.write(
         r"""if(PORT MATCHES "date")
     list(APPEND VCPKG_CMAKE_CONFIGURE_OPTIONS