The authors present the case of an 11-week-old girl in whom hydrocephalus developed secondary to intermittent obstruction of the third ventricle by a choroid plexus cyst. The patient presented to the emergency department at the authors' institution with a 1-day history of projectile vomiting, lethargy, and dysconjugate gaze. Hydrocephalus was confirmed on head CT. During hospitalization, the symptoms resolved with a decrease in ventricular size. One week later, the patient again presented with similar symptoms, and MR images with 3D-constructive interference in steady state sequences revealed that a cyst was blocking the third ventricle. The patient subsequently underwent endoscopic fenestration of the cyst with resolution of hydrocephalus and symptoms. The authors present a unique description of the diagnosis of intermittent obstructive hydrocephalus caused by a third ventricular region choroid plexus cyst in an infant.