Long-term management of patients with cloacal malformation is still challenging to pediatric surgeons and urologists. Recently, we experienced postoperative cystolithiasis in a case of cloacal malformation. All stones were removed successfully by using an endoscopic pneumatic lithotripter through a combined approach from the cystostomy and the narrow reconstructed urethra. To the best of our knowledge, this was the first time for this combined approach to be applied in a patient with cloacal malformation. It has a particular appeal because it is simple, safe, and minimally invasive.