Background Antenatally diagnosed abdominal cysts are common, and frequently are ovarian in origin, which usually regress spontaneously. Surgery is indicated in the infantile period in case of very large, persisting or symptomatic cysts. Many surgeons feel that watchful waiting can be justified in newborns with simple and complex cysts. Case We present a neonate with an ovarian cyst diagnosed antenatally by ultrasound (US) and showing persistent enlargement within 3 months after birth when reached a diameter of 13 cm. Assessment and treatment is described. Conclusion The extremely large, non-resolving ovarian cysts in neonates present a major challenge for clinicians and should be treated by surgery to avoid complications. We advocate laparotomy and cystectomy when possible to avoid unnecessary loss of functional ovarian tissue.