diff --git a/.github/workflows/auto-pr.yaml b/.github/workflows/auto-pr.yaml
index c83a234787..3cfc26c01c 100644
--- a/.github/workflows/auto-pr.yaml
+++ b/.github/workflows/auto-pr.yaml
@@ -46,6 +46,8 @@ jobs:
           echo -------------
 
           branches=$(ci/auto-pr/conv_proj_version_to_branch $versions)
+          # Remove the base branch from the list because the target change is already merged to the branch.
+          branches=$(echo "$branches" | sed "/^${{ github.base_ref }}$/d")
           echo -------------
           echo "branches: $branches"
           echo -------------
diff --git a/ci/auto-pr/conv_proj_version_to_branch b/ci/auto-pr/conv_proj_version_to_branch
index 8290baf29c..afb0f04f12 100755
--- a/ci/auto-pr/conv_proj_version_to_branch
+++ b/ci/auto-pr/conv_proj_version_to_branch
@@ -12,8 +12,7 @@ versions.inject(Set.new) {|acc, v|
       # e.g. project: "ScalarDB 4.0.0" -> branch: "master"
       #
       # This GitHub project corresponds to `main`/`master` branch.
-      # The target change is already merged to the default branch.
-      # Nonthing to do.
+      acc << "master"
     else
       # e.g. project: "ScalarDB 3.8.0" -> branch: "3"
       #