Seminal vesicle cyst with ipsilateral renal agenesis, even if rare in pediatric age, should be suspected in young male patients presenting with pelvic cystic masses, pelvic pain, dysuria, and ipsilateral renal absence. Conservative management should be reversed to asymptomatic patients. Surgical treatment is mandatory in symptomatic cases and the preferred approach is minimally invasive surgery to magnify the operating field to spare anatomical structures, primarily the contralateral vas deferens. Radicality is crucial to avoid the persistence of symptoms and the need for reintervention.