diff --git a/dev/builddeps-veloxbe.sh b/dev/builddeps-veloxbe.sh
index 3fcd42660f..2ae4451b5f 100755
--- a/dev/builddeps-veloxbe.sh
+++ b/dev/builddeps-veloxbe.sh
@@ -289,7 +289,7 @@ function get_velox {
 }
 
 function setup_dependencies {
-  DEPENDENCY_DIR=${DEPENDENCY_DIR:-$CURRENT_DIR/../ep/_ep}
+  export DEPENDENCY_DIR=${DEPENDENCY_DIR:-$CURRENT_DIR/../ep/_ep}
   mkdir -p ${DEPENDENCY_DIR}
 
   source $GLUTEN_DIR/dev/build-helper-functions.sh
@@ -297,6 +297,9 @@ function setup_dependencies {
 
   echo "Start to install dependencies"
   pushd $VELOX_HOME
+
+  # set GIT_CEILING_DIRECTORIES to make `git apply` work as expected.
+  export GIT_CEILING_DIRECTORIES=${DEPENDENCY_DIR}
   if [ $OS == 'Linux' ]; then
     setup_linux
   elif [ $OS == 'Darwin' ]; then
@@ -315,6 +318,8 @@ function setup_dependencies {
     export AZURE_SDK_DISABLE_AUTO_VCPKG=ON
     install_azure_storage_sdk_cpp
   fi
+  unset GIT_CEILING_DIRECTORIES
+
   popd
 }
 
diff --git a/dev/ci-velox-buildshared-centos-9.sh b/dev/ci-velox-buildshared-centos-9.sh
index d4008d125c..e47c1f72a4 100755
--- a/dev/ci-velox-buildshared-centos-9.sh
+++ b/dev/ci-velox-buildshared-centos-9.sh
@@ -24,5 +24,5 @@ if [ "$(uname -m)" = "aarch64" ]; then
     export VCPKG_FORCE_SYSTEM_BINARIES=1;
 fi
 
-./dev/builddeps-veloxbe.sh --run_setup_script=OFF --build_arrow=OFF --build_tests=ON \
+./dev/builddeps-veloxbe.sh --run_setup_script=ON --build_arrow=OFF --build_tests=ON \
     --build_examples=ON --build_benchmarks=ON
diff --git a/ep/build-velox/src/get-velox.sh b/ep/build-velox/src/get-velox.sh
index 71965f6c73..907167b3fe 100755
--- a/ep/build-velox/src/get-velox.sh
+++ b/ep/build-velox/src/get-velox.sh
@@ -18,8 +18,8 @@ set -exu
 
 CURRENT_DIR=$(cd "$(dirname "$BASH_SOURCE")"; pwd)
 VELOX_REPO=https://github.com/IBM/velox.git
-VELOX_BRANCH=dft-2026_06_06
-VELOX_ENHANCED_BRANCH=ibm-2026_06_06
+VELOX_BRANCH=dft-2026_06_12
+VELOX_ENHANCED_BRANCH=ibm-2026_06_12
 VELOX_HOME=""
 RUN_SETUP_SCRIPT=ON
 ENABLE_ENHANCED_FEATURES=OFF