diff --git a/setup/git_post_checkout_hook.py b/setup/git_post_checkout_hook.py
index 7d46791208..e482505771 100755
--- a/setup/git_post_checkout_hook.py
+++ b/setup/git_post_checkout_hook.py
@@ -25,5 +25,5 @@ if flags == '1':  # A branch checkout
     for dirpath, dirnames, filenames in os.walk('.'):
         for f in filenames:
             fpath = os.path.join(dirpath, f)
-            if f.endswith('.pyc'):
+            if f.endswith('.pyc') and '/chroot/' not in fpath:
                 os.remove(fpath)