A 67-year-old man presented with glossopharyngeal neuralgia (GPN) manifesting as severe paroxysmal pharyngeal and retroauricular pain not controlled by medical treatment. Constructive interference in steady state magnetic resonance imaging suggested that the responsible vessel was the right vertebral artery (VA). As carbamazepine had some limited effect, we reviewed the appropriateness of microvascular decompression surgery. Balloon test occlusion of the VA was performed to confirm that the GPN was due to right VA pulsation. The neuralgia disappeared and reappeared with balloon inflation and deflation. Therefore, the VA was moved to decompress the glossopharyngeal nerve. The patient was pain-free after surgery. Balloon test occlusion may be useful in the diagnosis of GPN and the selection of the most appropriate surgical treatment.