Ganglioglioma (GG) is a rare kind of intracranial tumor with low potential malignancy (WHO grade I), which could occur in any part of the brain. However, a patient with anaplastic ganglioglioma (WHO grade III) in the medulla oblongata is a more peculiar and rare clinical case. In our report, we presented a case of a 45-year-old man with anaplastic ganglioglioma (WHO grade III) in the medulla oblongata, who was perplexed with dysphagia, choking and left-sided numbness for two and a half years. The head magnetic resonance imaging (MRI) showed a 2.7 cm × 2.6 cm lesion in the medulla oblongata with slightly low signal on T1 weighted image (T1WI) and heterogeneous high signal without calcifications on T2 weighted image (T2WI). The Physical Examination manifested that the patient showed a chronic appearance, along with the damage of oculomotor nerve, glossopharyngeal and vagus nerves and spinal thalamus lateral tract and rope body. Subsequently, the patient underwent surgical and common radiotherapy treatment, which might delay the tumor recurrence and contribute to a better overall survival. Unexpectedly, tentative chemotherapy was carried out when the tumor showed the recurrence trend and anaplastic feature. Our presentation of this case would emphasize the rarity and significance of the diagnosis, differentiation and treatment of such tumors, demanding more clinical cases for exploration.