diff --git a/setup/git_post_checkout_hook.py b/setup/git_post_checkout_hook.py
index ccacb2e00f..9b34c85783 100755
--- a/setup/git_post_checkout_hook.py
+++ b/setup/git_post_checkout_hook.py
@@ -18,8 +18,9 @@ os.chdir(base)
 
 if flags == '1':  # A branch checkout
     prev_branch, cur_branch = list(map(get_branch_name, (prev_rev, current_rev)))
+    rebase_in_progress = os.path.exists('.git/rebase-apply') or os.path.exists('.git/rebase-merge')
 
-    if {prev_branch, cur_branch} == {'master', 'qt6'}:
+    if {prev_branch, cur_branch} == {'master', 'qt6'} and not rebase_in_progress:
         b = 'qt6' if cur_branch == 'qt6' else 'qt5'
         for x in os.listdir(f'bypy/b/{b}'):
             link = f'bypy/b/{x}'