A 20-day-old male neonate presented with fever and hydronephrosis. Evaluation revealed that the patient had a single left kidney and a rare combination of multiple congenital malformations: upper pole segmental multicystic dysplasia, ureteropelvic junction obstruction, and an obstructive and refluxing megaureter (ureterovesical junction obstruction). We performed percutaneous drainage of the infected and obstructed upper collecting system and then used a sequential approach to manage the patient's anomalies. First, we performed an upper pole partial nephrectomy and pyeloplasty with a modified Y ureterostomy. Second, when the child was older, we performed ureterovesical reimplantation with ureteral tailoring. Currently, after 5 years of follow up, the patient has stable renal function.