diff --git a/.github/workflows/native-windows.yml b/.github/workflows/native-windows.yml
index 2a8d0c22b6..10e889a943 100644
--- a/.github/workflows/native-windows.yml
+++ b/.github/workflows/native-windows.yml
@@ -382,13 +382,11 @@ jobs:
 
           # Needed for gendef tool in GoUtils.cmake
           pacman --noconfirm -S mingw-w64-x86_64-tools
-      # TODO(https://github.com/apache/arrow-adbc/issues/3825)
-      - name: Clone vcpkg
-        run: |
-          git clone https://github.com/microsoft/vcpkg.git
-          cd vcpkg
-          git checkout ef7dbf94b9198bc58f45951adcf1f041fcbc5ea0
-          .\bootstrap-vcpkg.bat
+      - name: Install vcpkg
+        shell: bash
+        env:
+          VCPKG_ROOT: ${{ github.workspace }}/vcpkg
+        run: ci/scripts/install_vcpkg.sh "$VCPKG_ROOT"
       - name: Install vcpkg dependencies
         working-directory: c
         env:
diff --git a/ci/scripts/install_vcpkg.sh b/ci/scripts/install_vcpkg.sh
index 1908fc541c..6af80b9217 100755
--- a/ci/scripts/install_vcpkg.sh
+++ b/ci/scripts/install_vcpkg.sh
@@ -27,7 +27,7 @@ if [ "$#" -lt 1 ]; then
 fi
 
 arrow_dir=$(cd -- "$(dirname -- "$0")/../.." && pwd -P)
-default_vcpkg_version=$(cat "${arrow_dir}/.env" | grep "VCPKG" | cut -d "=" -f2 | tr -d '"')
+default_vcpkg_version=$(cat "${arrow_dir}/.env" | grep "VCPKG" | cut -d "=" -f2 | awk '{print $1}' | tr -d '"')
 default_vcpkg_ports_patch="${arrow_dir}/ci/vcpkg/ports.patch"
 
 vcpkg_destination=$1
@@ -35,7 +35,7 @@ vcpkg_version=${2:-$default_vcpkg_version}
 vcpkg_ports_patch=${3:-$default_vcpkg_ports_patch}
 
 # reduce the fetched data using a shallow clone
-git clone --shallow-since=2025-09-01 https://github.com/microsoft/vcpkg ${vcpkg_destination}
+git clone --shallow-since=2026-05-01 https://github.com/microsoft/vcpkg ${vcpkg_destination}
 
 pushd ${vcpkg_destination}