diff --git a/ci/buildkite-pipeline-in-disk.sh b/ci/buildkite-pipeline-in-disk.sh
index 56c5b06201459e..bf9003106619a2 100644
--- a/ci/buildkite-pipeline-in-disk.sh
+++ b/ci/buildkite-pipeline-in-disk.sh
@@ -9,7 +9,13 @@ cd "$(dirname "$0")"/..
 output_file=${1:-/dev/stderr}
 
 if [[ -n $CI_PULL_REQUEST ]]; then
-  IFS=':' read -ra affected_files <<< "$(buildkite-agent meta-data get affected_files)"
+  # filter pr number from ci branch.
+  [[ $CI_BRANCH =~ pull/([0-9]+)/head ]]
+  pr_number=${BASH_REMATCH[1]}
+  echo "get affected files from PR: $pr_number"
+
+  # get affected files
+  readarray -t affected_files < <(gh pr diff --name-only "$pr_number")
   if [[ ${#affected_files[*]} -eq 0 ]]; then
     echo "Unable to determine the files affected by this PR"
     exit 1
diff --git a/ci/buildkite-pipeline.sh b/ci/buildkite-pipeline.sh
index 21f0b2a68c8ab8..e1c268ca2f9f76 100755
--- a/ci/buildkite-pipeline.sh
+++ b/ci/buildkite-pipeline.sh
@@ -9,7 +9,13 @@ cd "$(dirname "$0")"/..
 output_file=${1:-/dev/stderr}
 
 if [[ -n $CI_PULL_REQUEST ]]; then
-  IFS=':' read -ra affected_files <<< "$(buildkite-agent meta-data get affected_files)"
+  # filter pr number from ci branch.
+  [[ $CI_BRANCH =~ pull/([0-9]+)/head ]]
+  pr_number=${BASH_REMATCH[1]}
+  echo "get affected files from PR: $pr_number"
+
+  # get affected files
+  readarray -t affected_files < <(gh pr diff --name-only "$pr_number")
   if [[ ${#affected_files[*]} -eq 0 ]]; then
     echo "Unable to determine the files affected by this PR"
     exit 1
diff --git a/ci/buildkite-solana-private.sh b/ci/buildkite-solana-private.sh
index d05972808ae976..52249490b7ae32 100644
--- a/ci/buildkite-solana-private.sh
+++ b/ci/buildkite-solana-private.sh
@@ -9,7 +9,13 @@ cd "$(dirname "$0")"/..
 output_file=${1:-/dev/stderr}
 
 if [[ -n $CI_PULL_REQUEST ]]; then
-  IFS=':' read -ra affected_files <<< "$(buildkite-agent meta-data get affected_files)"
+  # filter pr number from ci branch.
+  [[ $CI_BRANCH =~ pull/([0-9]+)/head ]]
+  pr_number=${BASH_REMATCH[1]}
+  echo "get affected files from PR: $pr_number"
+
+  # get affected files
+  readarray -t affected_files < <(gh pr diff --name-only "$pr_number")
   if [[ ${#affected_files[*]} -eq 0 ]]; then
     echo "Unable to determine the files affected by this PR"
     exit 1