Endodermal cysts are rare congenital intracranial lesions. Although histologically benign, they can become symptomatic as a result of mass effect and cause neurological deficits. We report a 30-year-old woman who presented with paresis of her right oculomotor nerve. Magnetic resonance imaging showed a 13 x 8-mm cystic lesion originating from the right oculomotor nerve at its exit from the mesencephalon. She underwent craniotomy, biopsy, slit resection, and drainage of the cyst. To our knowledge, endodermal cysts have not been previously described in relation to the oculomotor nerve.