We present the case of a 30-year-old man who developed an acute hydrocephalus secondary to an obstruction of the cerebral aqueduct by a midbrain cystic lesion. After a ventriculo-peritoneal shunt was placed to relief symptoms of intracranial hypertension, the patient underwent a neuronavigation-assisted endoscopic fenestration of the cyst. A careful immunohistochemical staining confirmed the diagnosis of an ependymal cyst. An extensive review of the literature has revealed that this is the first report of a periaqueductal ependymal cyst with definite histological diagnosis. This is a rare cause of acute non-communicating hydrocephalus but an important entity in the differential diagnosis.