Brain stem gliomas (BSG) in adults are rare and less aggressive than those in children. However, the molecular profile of adult BSG cases has not been well characterized. We report a case of adult BSG with isocitrate dehydrogenase (IDH) mutation. A 43-year-old male was admitted to our hospital with diplopia and right-sided hypesthesia. An open biopsy led to the tumor being diagnosed as a diffuse astrocytoma. Immunohistochemically, the tumor was positive for IDH1 R132H, but negative for H3K27M. The patient received 54 Gy of local radiotherapy and adjuvant temozolomide, which resulted in the size of the lesion decreasing significantly. At 56 months after the initial diagnosis, the patient was referred to our hospital with a severe headache and ataxia. Magnetic resonance imaging (MRI) revealed a contrast-enhanced lesion in the brain stem, which extended into the left cerebellar hemisphere and brainstem. Partial tumor removal was performed, and a pathological examination revealed the features of glioblastoma. Immunohistochemically, the tumor was positive for IDH1 R132H and p53 and negative for ATRX. To the best of our knowledge, there are few reports about adult case of brain stem astrocytoma to be confirmed via histological and molecular examinations of the primary and recurrent tumor. We exhibit detailed pathological and molecular findings which resembles to IDH mutant supratentorial diffuse astrocytic tumors.