diff --git a/refs.c b/refs.c
index f0bd7ac0e9..130b89e92b 100644
--- a/refs.c
+++ b/refs.c
@@ -2353,7 +2353,8 @@ static void try_remove_empty_parents(char *name)
 /* make sure nobody touched the ref, and unlink */
 static void prune_ref(struct ref_to_prune *r)
 {
-	struct ref_lock *lock = lock_ref_sha1(r->name + 5, r->sha1);
+	struct ref_lock *lock = lock_any_ref_for_update(r->name, r->sha1,
+							0, NULL);
 
 	if (lock) {
 		unlink_or_warn(git_path("%s", r->name));
diff --git a/t/t3210-pack-refs.sh b/t/t3210-pack-refs.sh
index 1a2080e3dc..3a017bf437 100755
--- a/t/t3210-pack-refs.sh
+++ b/t/t3210-pack-refs.sh
@@ -151,4 +151,11 @@ test_expect_success 'delete ref while another dangling packed ref' '
 	test_cmp /dev/null result
 '
 
+test_expect_success 'pack ref directly below refs/' '
+	git update-ref refs/top HEAD &&
+	git pack-refs --all --prune &&
+	grep refs/top .git/packed-refs &&
+	test_path_is_missing .git/refs/top
+'
+
 test_done