Primary intracranial squamous cell carcinoma is extremely rare, with most cases arising from a preexisting benign epidermoid cyst. We report a rare case of primary intracranial squamous cell carcinoma in the brain stem with a cerebellopontine angle (CPA) epidermoid cyst. A 72-year-old female suffered from progressive left hemiparesis, difficulty in swallowing, and right hemifacial numbness. Diffusion-weighted magnetic resonance imaging revealed a high signal intensity (SI) lesion in the CPA region and an intra-axially ring-enhanced cystic mass in the right brain stem with low SI. Whole-body positron emission tomography showed no evidence of metastatic disease. The histological findings revealed a typical epidermoid cyst in the CPA region and a squamous cell carcinoma in the brain stem. We speculate that the squamous cell carcinoma may have been developed due to a chronic inflammatory response by the adjacent epidermoid cyst. The patient underwent a surgical resection and radiotherapy. After 12 months, she had no evidence of recurrence.