BackgroundEctopic scrotum (ES) is an extremely rare congenital scrotal malformation. Ectopic scrotum with VATER/VACTERL [vertebral defects (V), anal atresia or anorectal malformations (A), cardiac defects (C), tracheoesophageal fistula with or without esophageal atresia (TE), cardiac defects, renal malformations (R), and limb defects (L)] association is even rarer. There are no uniform guidelines for diagnosis and treatment.Clinical caseWe described a 2-year-5-month-old boy who has ectopic scrotum and penoscrotal transposition and reviewed relevant literature in this report. We performed laparoscopy exploration, rotation flap scrotoplasty, and orchiopexy and achieved a great result during the postoperative follow-up.ConclusionsCombined with the previous literature, we made a summary to come up with a plan for the diagnosis and treatment of ectopic scrotum. Rotation flap scrotoplasty and orchiopexy are worthy of considering operative methods in treating ES. For penoscrotal transposition or VATER/VACTERL association, we can treat the diseases individually.