diff --git a/cmake/external/onnxruntime_external_deps.cmake b/cmake/external/onnxruntime_external_deps.cmake
index e8f6bbe895d29..228906030d14c 100644
--- a/cmake/external/onnxruntime_external_deps.cmake
+++ b/cmake/external/onnxruntime_external_deps.cmake
@@ -774,13 +774,24 @@ if (onnxruntime_USE_WEBGPU)
   endif()
 
   if (NOT CMAKE_SYSTEM_NAME STREQUAL "Emscripten" AND onnxruntime_WGSL_TEMPLATE STREQUAL "dynamic")
-    onnxruntime_fetchcontent_declare(
-      duktape
-      URL ${DEP_URL_duktape}
-      URL_HASH SHA1=${DEP_SHA1_duktape}
-      EXCLUDE_FROM_ALL
-    )
-    onnxruntime_fetchcontent_makeavailable(duktape)
+    if(onnxruntime_USE_VCPKG)
+      find_package(unofficial-duktape CONFIG REQUIRED)
+      add_library(duktape_static ALIAS unofficial::duktape::duktape)
+    else()
+      onnxruntime_fetchcontent_declare(
+        duktape
+        URL ${DEP_URL_duktape}
+        URL_HASH SHA1=${DEP_SHA1_duktape}
+        EXCLUDE_FROM_ALL
+      )
+      onnxruntime_fetchcontent_makeavailable(duktape)
+
+      if(NOT TARGET duktape_static)
+        add_library(duktape_static STATIC "${duktape_SOURCE_DIR}/src/duktape.c")
+        target_compile_features(duktape_static PRIVATE c_std_99)
+        target_include_directories(duktape_static INTERFACE $<BUILD_INTERFACE:${duktape_SOURCE_DIR}/src>)
+      endif()
+    endif()
   endif()
 endif()
 
diff --git a/cmake/onnxruntime_providers_webgpu.cmake b/cmake/onnxruntime_providers_webgpu.cmake
index 5b80b1262464d..2865ad33b39f4 100644
--- a/cmake/onnxruntime_providers_webgpu.cmake
+++ b/cmake/onnxruntime_providers_webgpu.cmake
@@ -172,10 +172,12 @@
     file(MAKE_DIRECTORY ${WGSL_GENERATED_DIR})
 
     # Find all WGSL template input files
-    file(GLOB_RECURSE WGSL_TEMPLATE_FILES "${ONNXRUNTIME_ROOT}/core/providers/webgpu/*.wgsl.template")
+    file(GLOB_RECURSE WGSL_TEMPLATE_FILES
+      "${ONNXRUNTIME_ROOT}/core/providers/webgpu/*.wgsl.template"
+      "${ONNXRUNTIME_ROOT}/contrib_ops/webgpu/*.wgsl.template")
 
     # Set wgsl-gen command line options as a list
-    set(WGSL_GEN_OPTIONS "-i" "../" "--output" "${WGSL_GENERATED_DIR}" "-I" "wgsl_template_gen/" "--preserve-code-ref" "--verbose")
+    set(WGSL_GEN_OPTIONS "-i" "${ONNXRUNTIME_ROOT}/core/providers/webgpu/" "-i" "${ONNXRUNTIME_ROOT}/contrib_ops/webgpu/" "--output" "${WGSL_GENERATED_DIR}" "-I" "wgsl_template_gen/" "--preserve-code-ref" "--verbose")
     if (onnxruntime_WGSL_TEMPLATE STREQUAL "static")
       if (CMAKE_BUILD_TYPE STREQUAL "Debug")
         list(APPEND WGSL_GEN_OPTIONS "--generator" "static-cpp-literal")
@@ -207,10 +209,9 @@
       # Add the generated directory to include paths
       target_include_directories(onnxruntime_providers_webgpu PRIVATE ${WGSL_GENERATED_ROOT})
     elseif(onnxruntime_WGSL_TEMPLATE STREQUAL "dynamic")
-      add_library(duktape_static STATIC "${duktape_SOURCE_DIR}/src/duktape.c")
-      target_compile_features(duktape_static PRIVATE c_std_99)
       target_link_libraries(onnxruntime_providers_webgpu duktape_static)
-      target_include_directories(onnxruntime_providers_webgpu PRIVATE ${duktape_SOURCE_DIR}/src)
+      onnxruntime_add_include_to_target(onnxruntime_providers_webgpu duktape_static)
+
       # Define the path to the generated templates.js file
       target_compile_definitions(onnxruntime_providers_webgpu PRIVATE
         "ORT_WGSL_TEMPLATES_JS_PATH=\"${WGSL_GENERATED_TEMPLATES_JS}\"")
diff --git a/cmake/vcpkg.json b/cmake/vcpkg.json
index 7c6b2fed36d1b..7f14fe6d04cef 100644
--- a/cmake/vcpkg.json
+++ b/cmake/vcpkg.json
@@ -94,6 +94,10 @@
     "webgpu-ep": {
       "description": "Build with WebGPU EP",
       "dependencies": []
+    },
+    "webgpu-ep-wgsl-template-dynamic": {
+      "description": "Build with WebGPU EP with dynamic WGSL template code generator",
+      "dependencies": ["duktape"]
     }
   },
   "overrides": [
@@ -104,6 +108,10 @@
     {
       "name": "flatbuffers",
       "version": "23.5.26"
+    },
+    {
+      "name": "duktape",
+      "version": "2.7.0#2"
     }
   ]
 }
diff --git a/onnxruntime/core/providers/webgpu/wgsl_templates/package-lock.json b/onnxruntime/core/providers/webgpu/wgsl_templates/package-lock.json
index 7cde6c17f54e9..df1940ed6416b 100644
--- a/onnxruntime/core/providers/webgpu/wgsl_templates/package-lock.json
+++ b/onnxruntime/core/providers/webgpu/wgsl_templates/package-lock.json
@@ -9,13 +9,13 @@
       "version": "1.0.0",
       "license": "MIT",
       "dependencies": {
-        "@fs-eire/wgsl-template": "^0.1.3"
+        "@fs-eire/wgsl-template": "^0.1.13"
       }
     },
     "node_modules/@fs-eire/wgsl-template": {
-      "version": "0.1.10",
-      "resolved": "https://registry.npmjs.org/@fs-eire/wgsl-template/-/wgsl-template-0.1.10.tgz",
-      "integrity": "sha512-F5qQZxNweZ3ZD3d9RNc/g3nTiW7jyaAVi7SlMOL4wOfXh+Nm/qca2DISNTf3kjpVqkoazMJGbZ6TPQ4a/vjw0g==",
+      "version": "0.1.13",
+      "resolved": "https://registry.npmjs.org/@fs-eire/wgsl-template/-/wgsl-template-0.1.13.tgz",
+      "integrity": "sha512-SOQjVCQCUmXb9qYr2E3CKNs88/FzINuhFJiobBEkSAsyKtJby9oFWGZnrEO+hIl/oDTLA01LbjiDxuf6TGHE/w==",
       "license": "MIT",
       "dependencies": {
         "minimist": "^1.2.8"
diff --git a/onnxruntime/core/providers/webgpu/wgsl_templates/package.json b/onnxruntime/core/providers/webgpu/wgsl_templates/package.json
index 34831ccddeb33..246e7365531e0 100644
--- a/onnxruntime/core/providers/webgpu/wgsl_templates/package.json
+++ b/onnxruntime/core/providers/webgpu/wgsl_templates/package.json
@@ -10,6 +10,6 @@
   "author": "",
   "license": "MIT",
   "dependencies": {
-    "@fs-eire/wgsl-template": "^0.1.3"
+    "@fs-eire/wgsl-template": "^0.1.13"
   }
 }
diff --git a/tools/ci_build/build.py b/tools/ci_build/build.py
index f6e37d33b2414..f864b8eb4a74d 100644
--- a/tools/ci_build/build.py
+++ b/tools/ci_build/build.py
@@ -284,6 +284,8 @@ def generate_vcpkg_install_options(build_dir, args):
         vcpkg_install_options.append("--x-feature=vsinpu-ep")
     if args.use_webgpu:
         vcpkg_install_options.append("--x-feature=webgpu-ep")
+        if args.wgsl_template == "dynamic":
+            vcpkg_install_options.append("--x-feature=webgpu-ep-wgsl-template-dynamic")
     if args.use_webnn:
         vcpkg_install_options.append("--x-feature=webnn-ep")
     if args.use_xnnpack: