A 3.5-year-old boy was admitted with febrile convulsion for the first time. The patient had a medical history of in vitro fertilization (IVF) and premature delivery in the 21st week of pregnancy. Further, he suffered from neonatal germinal matrix hemorrhage and intraventricular hematoma (IVH). The patient was treated in the pediatric intensive care unit. Cranial magnetic resonance imaging (MRI) showed resorption of the hematoma with the presence of cavum vergae (CV) variation. The new brain MRI revealed progression of the cavum to a large CV cyst compared with the previous imagings, causing pressure upon both lateral ventricles. Endoscopic fenestration of the lateral walls of the cyst with lateral ventricles was performed. The postoperative period was uneventful and the patient was discharged the next day. Followup MRI one year after surgery showed normal ventricle size, shrinkage of the cyst and cerebrospinal fluid (CSF) flow between the cyst and the lateral ventricles. This is an interesting demonstration of the progression over years of a CV anatomical variation to a large CV cyst in a premature birth case that experienced germinal matrix hemorrhage.