Brainstem epidermoid cysts are rare lesions, with only 18 reported cases in the literature and only five purely intrinsic epidermoid cysts within this group. The authors present the case of a 3-year-old girl with a history of chronic headaches, progressive diplopia, and relapsing and remitting mild right hemiparesis who was found to harbor an intrinsic brainstem epidermoid cyst at the pontomedullary junction. Initial working diagnoses included intrinsic brainstem astrocytoma and cavernoma. After tumor enlargement and progressive symptoms, a diffusion-weighted (DW) magnetic resonance (MR) imaging sequence was performed and a definitive diagnosis of an intrinsic brainstem epidermoid cyst was made in the patient. The patient underwent a suboccipital craniotomy and complete resection of the cyst with the aid of intraoperative neurophysiological monitoring. Three years after the operation, the patient is neurologically intact and no evidence of tumor recurrence has been found. The rarity of brainstem epidermoid cysts can make their diagnosis difficult; thus a DW MR imaging sequence of the brain is a useful diagnostic modality. Intrinsic brainstem epidermoid cysts can be removed safely, in a manner similar to that used for the surgical treatment of focal tumors.