diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 1e743f55f..8ed489f9d 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -60,6 +60,9 @@ jobs:
           New-Item -Path "C:\" -Name "tmp" -ItemType Directory
           echo "TMPDIR=c:\tmp" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
 
+      - name: Run StanHeaders cleanup script
+        run: cd StanHeaders && bash -x ./cleanup
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           working-directory: rstan/rstan