This report describes a neonatal case in whom a large interhemispheric cyst associated with agenesis of the corpus callosum was revealed by fetal ultrasonography and demonstrated by MRI to be multilobulated. Endoscopic fenestration of cysts was initially designed in view of the development of the patient’s brain and surgical invasiveness. One year later, when motor paresis of the left arm and progressive enlargement of the cyst on MRI were revealed, open surgery was performed. The histological diagnosis was a neuroepithelial cyst with the feature of choroid plexus epithelia. The clinicopathological features of interhemispheric epithelial cysts associated with agenesis of the corpus callosum are reviewed in the light of differential diagnosis and therapeutic considerations.