diff --git a/.github/workflows/size.yml b/.github/workflows/size.yml
index a195681f9..596f2f26f 100644
--- a/.github/workflows/size.yml
+++ b/.github/workflows/size.yml
@@ -44,8 +44,6 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: true
     - name: Bootstrap
       if: "github.event_name == 'push'"
       run: |
@@ -55,6 +53,7 @@ jobs:
       env:
         OT_BASE_BRANCH: "${{ github.base_ref }}"
         SIZE_REPORT_URL: "https://openthread-size-report.glitch.me/size-report/1354027"
+        GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       run: |
         export PATH=$PATH:$HOME/.local/bin
         ./script/check-size
diff --git a/script/check-size b/script/check-size
index 17deb26fe..bf9f2345b 100755
--- a/script/check-size
+++ b/script/check-size
@@ -157,7 +157,7 @@ size_nrf52840_version()
 
     # new commit
     mkdir -p "${OT_TMP_DIR}/b"
-    git clone https://github.com/openthread/ot-nrf528xx.git "${OT_TMP_DIR}/b"
+    script/git-tool clone https://github.com/openthread/ot-nrf528xx.git "${OT_TMP_DIR}/b"
     rm -rf "${OT_TMP_DIR}/b/openthread/*" # replace openthread submodule with latest commit
     git archive "${OT_SHA_NEW}" | tar x -C "${OT_TMP_DIR}/b/openthread"
 
diff --git a/script/git-tool b/script/git-tool
index 4cf8ba175..5acb5c75e 100755
--- a/script/git-tool
+++ b/script/git-tool
@@ -38,13 +38,12 @@ apply_dependencies()
 
     project_name=$(git remote get-url origin | grep -oE '[^/:]+/[^/:]+\.git$' | cut -d. -f1)
     echo "project name: ${project_name}"
-    depends_on_pr="$(grep -E "^Depends-On: *${project_name}" | cut -d# -f2)" || {
-        echo "No dependency on ${project_name} found."
-        return 0
-    }
-    echo "pr: #${depends_on_pr}"
-    git fetch --depth 1 origin "pull/${depends_on_pr}/head"
-    git checkout FETCH_HEAD
+    while read -r dependency; do
+        echo "${dependency}"
+        depends_on_pr="$(echo "${dependency}" | tr -d '\r\n' | cut -d# -f2)"
+        echo "pr: #${depends_on_pr}"
+        git pull origin "pull/${depends_on_pr}/merge"
+    done < <(grep -E "^Depends-On: *${project_name}" || true)
 }
 
 get_pr_body()