diff --git a/.github/workflows/mac.yml b/.github/workflows/mac.yml
index b36b0aa555940..04b5fdb85ed56 100644
--- a/.github/workflows/mac.yml
+++ b/.github/workflows/mac.yml
@@ -117,17 +117,21 @@ jobs:
       with:
         python-version: ${{ env.python_version }}
 
+    - name: "Run Homebrew"
+      run: brew install autoconf automake autoconf-archive
+
     - name: "Run vcpkg(x64-osx)"
       uses: lukka/run-vcpkg@v11
       with:
         vcpkgDirectory: "${{ runner.temp }}/vcpkg"
-        vcpkgGitCommitId: "1de2026f28ead93ff1773e6e680387643e914ea1" # 2024.07.12
-        runVcpkgInstall: true
+        vcpkgGitCommitId: "b322364f06308bdd24823f9d8f03fe0cc86fd46f" # 2024.12.16
+        runVcpkgInstall: true # vcpkg install --x-manifest-root cmake --x-install-root .build --overlay-triplets cmake/vcpkg-triplets
         vcpkgJsonGlob: "cmake/vcpkg.json"
         vcpkgConfigurationJsonGlob: "cmake/vcpkg-configuration.json"
       env:
         VCPKG_INSTALLED_DIR: "${{ github.workspace }}/.build"
         VCPKG_DEFAULT_TRIPLET: "x64-osx"
+        VCPKG_OVERLAY_TRIPLETS: "${{ github.workspace }}/cmake/vcpkg-triplets"
         # VCPKG_BINARY_SOURCES: "default" # https://learn.microsoft.com/en-us/vcpkg/reference/binarycaching
 
     - name: "Run compile_schema.py"
@@ -163,19 +167,22 @@ jobs:
           --cmake_extra_defines "VCPKG_TARGET_TRIPLET=x64-osx" \
           --cmake_extra_defines "VCPKG_INSTALLED_DIR:PATH=${{ github.workspace }}/.build" \
           --cmake_extra_defines "VCPKG_INSTALL_OPTIONS=--x-feature=tests"
+      env:
+        VCPKG_OVERLAY_TRIPLETS: "${{ github.workspace }}/cmake/vcpkg-triplets"
       shell: bash
 
     - name: "Run vcpkg(arm64-osx)"
       uses: lukka/run-vcpkg@v11
       with:
         vcpkgDirectory: "${{ runner.temp }}/vcpkg"
-        vcpkgGitCommitId: "1de2026f28ead93ff1773e6e680387643e914ea1" # 2024.07.12
-        runVcpkgInstall: true
+        doNotUpdateVcpkg: true
+        runVcpkgInstall: true # vcpkg install --x-manifest-root cmake --x-install-root .build --overlay-triplets cmake/vcpkg-triplets
         vcpkgJsonGlob: "cmake/vcpkg.json"
         vcpkgConfigurationJsonGlob: "cmake/vcpkg-configuration.json"
       env:
         VCPKG_INSTALLED_DIR: "${{ github.workspace }}/.build"
         VCPKG_DEFAULT_TRIPLET: "arm64-osx"
+        VCPKG_OVERLAY_TRIPLETS: "${{ github.workspace }}/cmake/vcpkg-triplets"
         # VCPKG_BINARY_SOURCES: "default" # https://learn.microsoft.com/en-us/vcpkg/reference/binarycaching
 
     - name: "Run build.py(arm64-osx)"
@@ -193,6 +200,8 @@ jobs:
           --cmake_extra_defines "VCPKG_TARGET_TRIPLET=arm64-osx" \
           --cmake_extra_defines "VCPKG_INSTALLED_DIR:PATH=${{ github.workspace }}/.build" \
           --cmake_extra_defines "VCPKG_INSTALL_OPTIONS=--x-feature=tests"
+      env:
+        VCPKG_OVERLAY_TRIPLETS: "${{ github.workspace }}/cmake/vcpkg-triplets"
       shell: bash
 
   Objective-C-StaticAnalysis:
diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
index 8a95e8a7b7b89..0f73aaac60014 100644
--- a/.github/workflows/windows.yml
+++ b/.github/workflows/windows.yml
@@ -56,12 +56,14 @@ jobs:
         uses: lukka/run-vcpkg@v11
         with:
           vcpkgDirectory: "C:/vcpkg" # use VCPKG_INSTALLATION_ROOT of the image
-          runVcpkgInstall: true
+          vcpkgGitCommitId: "b322364f06308bdd24823f9d8f03fe0cc86fd46f" # 2024.12.16
+          runVcpkgInstall: true # vcpkg install --x-manifest-root cmake --x-install-root .build --overlay-triplets cmake/vcpkg-triplets
           vcpkgJsonGlob: "cmake/vcpkg.json"
           vcpkgConfigurationJsonGlob: "cmake/vcpkg-configuration.json"
         env:
           VCPKG_INSTALLED_DIR: "${{ github.workspace }}/.build"
           VCPKG_DEFAULT_TRIPLET: "x64-windows"
+          VCPKG_OVERLAY_TRIPLETS: "${{ github.workspace }}/cmake/vcpkg-triplets"
           # VCPKG_BINARY_SOURCES: "default" # https://learn.microsoft.com/en-us/vcpkg/reference/binarycaching
 
       - name: "Run compile_schema.py"
@@ -99,6 +101,8 @@ jobs:
             --cmake_extra_defines "VCPKG_TARGET_TRIPLET=x64-windows" `
             --cmake_extra_defines "VCPKG_INSTALLED_DIR:PATH=${{ github.workspace }}/.build" `
             --cmake_extra_defines "VCPKG_INSTALL_OPTIONS=--x-feature=tests"
+        env:
+          VCPKG_OVERLAY_TRIPLETS: "${{ github.workspace }}/cmake/vcpkg-triplets"
         shell: pwsh
 
       - name: "Run vcpkg(arm64-windows)"
@@ -106,12 +110,13 @@ jobs:
         with:
           vcpkgDirectory: "C:/vcpkg" # use VCPKG_INSTALLATION_ROOT of the image
           doNotUpdateVcpkg: true
-          runVcpkgInstall: true
+          runVcpkgInstall: true # vcpkg install --x-manifest-root cmake --x-install-root .build --overlay-triplets cmake/vcpkg-triplets
           vcpkgJsonGlob: "cmake/vcpkg.json"
           vcpkgConfigurationJsonGlob: "cmake/vcpkg-configuration.json"
         env:
           VCPKG_INSTALLED_DIR: "${{ github.workspace }}/.build"
           VCPKG_DEFAULT_TRIPLET: "arm64-windows"
+          VCPKG_OVERLAY_TRIPLETS: "${{ github.workspace }}/cmake/vcpkg-triplets"
           # VCPKG_BINARY_SOURCES: "default" # https://learn.microsoft.com/en-us/vcpkg/reference/binarycaching
 
       - name: "Run build.py(arm64-windows)"
@@ -128,4 +133,6 @@ jobs:
             --cmake_extra_defines "VCPKG_TARGET_TRIPLET=arm64-windows" `
             --cmake_extra_defines "VCPKG_INSTALLED_DIR:PATH=${{ github.workspace }}/.build" `
             --cmake_extra_defines "VCPKG_INSTALL_OPTIONS=--x-feature=tests"
+        env:
+          VCPKG_OVERLAY_TRIPLETS: "${{ github.workspace }}/cmake/vcpkg-triplets"
         shell: pwsh
diff --git a/cmake/CMakePresets.json b/cmake/CMakePresets.json
index 1b7aa11975a3e..4987edaf85513 100644
--- a/cmake/CMakePresets.json
+++ b/cmake/CMakePresets.json
@@ -14,6 +14,7 @@
                 "VCPKG_INSTALLED_DIR": "${sourceParentDir}/.build"
             },
             "environment": {
+                "VCPKG_OVERLAY_TRIPLETS": "${sourceDir}/vcpkg-triplets",
                 "VCPKG_FEATURE_FLGAS": "manifests,versions"
             }
         },
diff --git a/cmake/vcpkg-configuration.json b/cmake/vcpkg-configuration.json
index 4afc30a3b969d..89954eaec9afd 100644
--- a/cmake/vcpkg-configuration.json
+++ b/cmake/vcpkg-configuration.json
@@ -2,7 +2,7 @@
     "default-registry": {
         "kind": "git",
         "repository": "https://github.com/Microsoft/vcpkg",
-        "baseline": "c82f74667287d3dc386bce81e44964370c91a289"
+        "baseline": "93570a28ecdf49d3d9676cec8aa0cc72935d43db"
     },
     "registries": []
 }
diff --git a/cmake/vcpkg-triplets/arm64-osx.cmake b/cmake/vcpkg-triplets/arm64-osx.cmake
new file mode 100644
index 0000000000000..543081c5073c4
--- /dev/null
+++ b/cmake/vcpkg-triplets/arm64-osx.cmake
@@ -0,0 +1,14 @@
+# https://learn.microsoft.com/en-us/vcpkg/users/triplets
+set(VCPKG_TARGET_ARCHITECTURE arm64)
+set(VCPKG_CRT_LINKAGE dynamic)
+set(VCPKG_LIBRARY_LINKAGE static)
+
+set(VCPKG_CMAKE_SYSTEM_NAME Darwin)
+set(VCPKG_OSX_ARCHITECTURES arm64)
+
+# provide build options for vcpkg installed packages
+if(PORT MATCHES "onnx")
+    list(APPEND VCPKG_CMAKE_CONFIGURE_OPTIONS
+        "-DONNX_DISABLE_STATIC_REGISTRATION=ON"
+    )
+endif()
diff --git a/cmake/vcpkg-triplets/arm64-windows.cmake b/cmake/vcpkg-triplets/arm64-windows.cmake
new file mode 100644
index 0000000000000..13caf5a12f72b
--- /dev/null
+++ b/cmake/vcpkg-triplets/arm64-windows.cmake
@@ -0,0 +1,11 @@
+# https://learn.microsoft.com/en-us/vcpkg/users/triplets
+set(VCPKG_TARGET_ARCHITECTURE arm64)
+set(VCPKG_CRT_LINKAGE dynamic)
+set(VCPKG_LIBRARY_LINKAGE dynamic)
+
+# provide build options for vcpkg installed packages
+if(PORT MATCHES "onnx")
+    list(APPEND VCPKG_CMAKE_CONFIGURE_OPTIONS
+        "-DONNX_DISABLE_STATIC_REGISTRATION=ON"
+    )
+endif()
diff --git a/cmake/vcpkg-triplets/x64-osx.cmake b/cmake/vcpkg-triplets/x64-osx.cmake
new file mode 100644
index 0000000000000..be656a060490c
--- /dev/null
+++ b/cmake/vcpkg-triplets/x64-osx.cmake
@@ -0,0 +1,14 @@
+# https://learn.microsoft.com/en-us/vcpkg/users/triplets
+set(VCPKG_TARGET_ARCHITECTURE x64)
+set(VCPKG_CRT_LINKAGE dynamic)
+set(VCPKG_LIBRARY_LINKAGE static)
+
+set(VCPKG_CMAKE_SYSTEM_NAME Darwin)
+set(VCPKG_OSX_ARCHITECTURES x86_64)
+
+# provide build options for vcpkg installed packages
+if(PORT MATCHES "onnx")
+    list(APPEND VCPKG_CMAKE_CONFIGURE_OPTIONS
+        "-DONNX_DISABLE_STATIC_REGISTRATION=ON"
+    )
+endif()
diff --git a/cmake/vcpkg-triplets/x64-windows.cmake b/cmake/vcpkg-triplets/x64-windows.cmake
new file mode 100644
index 0000000000000..ee137a9586a7d
--- /dev/null
+++ b/cmake/vcpkg-triplets/x64-windows.cmake
@@ -0,0 +1,11 @@
+# https://learn.microsoft.com/en-us/vcpkg/users/triplets
+set(VCPKG_TARGET_ARCHITECTURE x64)
+set(VCPKG_CRT_LINKAGE dynamic)
+set(VCPKG_LIBRARY_LINKAGE dynamic)
+
+# provide build options for vcpkg installed packages
+if(PORT MATCHES "onnx")
+    list(APPEND VCPKG_CMAKE_CONFIGURE_OPTIONS
+        "-DONNX_DISABLE_STATIC_REGISTRATION=ON"
+    )
+endif()
diff --git a/cmake/vcpkg.json b/cmake/vcpkg.json
index fcb2c7d5de89b..e874c29a13f1c 100644
--- a/cmake/vcpkg.json
+++ b/cmake/vcpkg.json
@@ -30,15 +30,15 @@
     },
     "ms-gsl",
     "nlohmann-json",
-    {
-      "name": "nsync",
-      "platform": "!windows"
-    },
     {
       "name": "nsync",
       "platform": "!windows",
       "version>=": "1.26.0"
     },
+    {
+      "name": "onnx",
+      "version>=": "1.16.2"
+    },
     "optional-lite",
     {
       "name": "protobuf",
@@ -66,12 +66,6 @@
       "platform": "windows"
     }
   ],
-  "overrides": [
-    {
-      "name": "flatbuffers",
-      "version": "23.5.26"
-    }
-  ],
   "features": {
     "tests": {
       "description": "Build ONNXRuntime unit tests",
@@ -80,5 +74,15 @@
         "gtest"
       ]
     }
-  }
+  },
+  "overrides": [
+    {
+      "name": "protobuf",
+      "version": "3.21.12#4"
+    },
+    {
+      "name": "flatbuffers",
+      "version": "23.5.26"
+    }
+  ]
 }