Glossopharyngeal neuralgia is a relatively rare condition characterized by severe, paroxysmal episodes of lancinating pain in the tongue, throat, ear, and tonsil. This disorder is assumed to be due to compression of the glossopharyngeal nerve by vascular structures. A 47-year-old woman complaining of sharp and lancinating pain in the right periauricular and submandibular areas visited our hospital. Swallowing, chewing, and lying on her right side triggered the pain. Her neurologic examination revealed no specific abnormalities. The results of routine hematologic and blood chemistry studies were all within normal limits. Carbamazepine and gabapentin were given, but her symptoms persisted. Her pain was temporarily relieved only by narcotic pain medication. MRI showed an arachnoid cyst located in the right cerebellomedullary cistern extending to the cerebellopontine cistern. Cyst removal was performed via a right retrosigmoid approach. Lateral suboccipital craniotomy was performed using the right park-bench position. After opening the dura and cerebellopontine angle, the arachnoid cyst was exposed. The arachnoid cyst was compressing the flattened lower cranial nerves at the right jugular fossa. Her symptoms resolved postoperatively. Two months after the operation, she was completely free from her previous symptoms.