diff --git a/src/submodule.c b/src/submodule.c
index 38db41529..3f39b9ef0 100644
--- a/src/submodule.c
+++ b/src/submodule.c
@@ -80,7 +80,8 @@ static kh_inline int str_equal_no_trailing_slash(const char *a, const char *b)
 	if (blen > 0 && b[blen - 1] == '/')
 		blen--;
 
-	return (alen == blen && strncmp(a, b, alen) == 0);
+	return (alen == 0 && blen == 0) ||
+		(alen == blen && strncmp(a, b, alen) == 0);
 }
 
 __KHASH_IMPL(