diff --git a/sequencer.c b/sequencer.c
index bec191aa69..98b41ae890 100644
--- a/sequencer.c
+++ b/sequencer.c
@@ -3434,6 +3434,7 @@ static int pick_commits(struct todo_list *todo_list, struct replay_opts *opts)
 			unlink(rebase_path_author_script());
 			unlink(rebase_path_stopped_sha());
 			unlink(rebase_path_amend());
+			unlink(git_path_merge_head(the_repository));
 			delete_ref(NULL, "REBASE_HEAD", NULL, REF_NO_DEREF);
 		}
 		if (item->command <= TODO_SQUASH) {
@@ -3790,6 +3791,7 @@ static int commit_staged_changes(struct replay_opts *opts,
 			   opts, flags))
 		return error(_("could not commit staged changes."));
 	unlink(rebase_path_amend());
+	unlink(git_path_merge_head(the_repository));
 	if (final_fixup) {
 		unlink(rebase_path_fixup_msg());
 		unlink(rebase_path_squash_msg());