diff --git a/cgmanifests/submodules/cgmanifest.json b/cgmanifests/submodules/cgmanifest.json
index a75ed5205ebd6..8b3cc066f25c7 100644
--- a/cgmanifests/submodules/cgmanifest.json
+++ b/cgmanifests/submodules/cgmanifest.json
@@ -352,7 +352,7 @@
       "component": {
         "type": "git",
         "git": {
-          "commitHash": "436bd7880e458532901c58f4d9d1ea23fa7edd52",
+          "commitHash": "2dc747c574b68a808ea4699d26942c8132fe2b09",
           "repositoryUrl": "https://github.com/protocolbuffers/protobuf.git"
         },
         "comments": "git submodule at cmake/external/protobuf"
diff --git a/cmake/external/protobuf b/cmake/external/protobuf
index 436bd7880e458..2dc747c574b68 160000
--- a/cmake/external/protobuf
+++ b/cmake/external/protobuf
@@ -1 +1 @@
-Subproject commit 436bd7880e458532901c58f4d9d1ea23fa7edd52
+Subproject commit 2dc747c574b68a808ea4699d26942c8132fe2b09
diff --git a/tools/ci_build/github/azure-pipelines/templates/py-packaging-stage.yml b/tools/ci_build/github/azure-pipelines/templates/py-packaging-stage.yml
index e52c817cd4e44..6ea9f6821e12b 100644
--- a/tools/ci_build/github/azure-pipelines/templates/py-packaging-stage.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/py-packaging-stage.yml
@@ -1070,8 +1070,8 @@ stages:
             sudo rm -rf /mnt/toolchains
             sudo mkdir /mnt/toolchains
             sudo tar -Jxf $(Build.BinariesDirectory)/toolchains.tar.xz -C /mnt/toolchains
-            aria2c -q https://github.com/protocolbuffers/protobuf/releases/download/v3.15.8/protoc-3.15.8-linux-x86_64.zip
-            unzip protoc-3.15.8-linux-x86_64.zip
+            aria2c -q https://github.com/protocolbuffers/protobuf/releases/download/v3.16.0/protoc-3.16.0-linux-x86_64.zip
+            unzip protoc-3.16.0-linux-x86_64.zip
             sudo cp /mnt/toolchains/manylinux2014_aarch64/usr/include/stdlib.h /mnt/toolchains/gcc-linaro-7.5.0-2019.12-x86_64_aarch64-linux-gnu/aarch64-linux-gnu/libc/usr/include/
             #The PYTHON_EXECUTABLE cmake variable is only used for generating ONNX's protobuf definition file.(Invoking the onnx/gen_proto.py file in ONNX's source folder)
             cmake \
diff --git a/tools/ci_build/github/linux/docker/scripts/install_protobuf.sh b/tools/ci_build/github/linux/docker/scripts/install_protobuf.sh
index 23e82550d977b..1831ea22fc56f 100755
--- a/tools/ci_build/github/linux/docker/scripts/install_protobuf.sh
+++ b/tools/ci_build/github/linux/docker/scripts/install_protobuf.sh
@@ -34,9 +34,9 @@ function GetFile {
   return $?
 }
 
-GetFile https://github.com/protocolbuffers/protobuf/archive/v3.15.8.tar.gz /tmp/src/v3.15.8.tar.gz
-tar -xf /tmp/src/v3.15.8.tar.gz -C /tmp/src
-cd /tmp/src/protobuf-3.15.8
+GetFile https://github.com/protocolbuffers/protobuf/archive/v3.16.0.tar.gz /tmp/src/v3.16.0.tar.gz
+tar -xf /tmp/src/v3.16.0.tar.gz -C /tmp/src
+cd /tmp/src/protobuf-3.16.0
 cmake ./cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_POSITION_INDEPENDENT_CODE=ON -Dprotobuf_BUILD_TESTS=OFF -DCMAKE_BUILD_TYPE=Relwithdebinfo
 make -j$(getconf _NPROCESSORS_ONLN)
 make install
diff --git a/tools/ci_build/github/linux/docker/scripts/install_server_deps.sh b/tools/ci_build/github/linux/docker/scripts/install_server_deps.sh
index 1458f6d83fc65..5e7f7c3b82f10 100755
--- a/tools/ci_build/github/linux/docker/scripts/install_server_deps.sh
+++ b/tools/ci_build/github/linux/docker/scripts/install_server_deps.sh
@@ -42,7 +42,7 @@ rm -rf /tmp/googletest
 echo "Installing protobuf from source"
 git clone https://github.com/protocolbuffers/protobuf.git
 cd protobuf
-git checkout v3.15.8
+git checkout v3.16.0
 mkdir b
 cd b
 cmake ../cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_POSITION_INDEPENDENT_CODE=ON -Dprotobuf_BUILD_TESTS=OFF -DCMAKE_BUILD_TYPE=Debug