Percutaneous nephrolithotomy (PCNL) is a difficult treatment for treating kidney stones, especially when there are orthopedic or skeletal abnormalities. Here, in a 19-year-old male, we describe a two-step PCNL with a case of caudal regression syndrome (CRS) and a pelvic kidney, with an extremely deformed neurogenic bladder on intermittent catheterization. Our conclusion is that PCNL may be done safely with minimum morbidity in patients with caudal regression syndrome by utilizing adult equipment for heavy stone burdens, allowing full and rapid stone removal.