Glioependymal cysts are a rare, congenital, and benign condition. The authors report a case of a 2-year-old female patient who presented with a large exophytic glioependymal cyst located in the left cerebral peduncle, which began with a history of deteriorating function of the left third cranial nerve (CN III). A left 3-piece fronto-orbitozygomatic approach and a microsurgical complete excision of the cyst were performed without complications by accessing the midbrain through the perioculomotor entry zone. The patient’s CN III function completely recovered after 3 months. Because there are currently no widely approved and used classification systems for these cysts, their reporting, naming, and classification are quite confusing in the literature. Thus, their origin, classification, and most common locations warrant further investigation. In addition to reporting this case, the authors present their review of the literature.