We report a case of successfully treated glossopharyngeal neuralgia, in whom preoperative magnetic resonance imaging (MRI) with a sequence of constructive interference in steady-state (CISS) precisely delineated microvascular compression to the glossopharyngeal nerve at its cisternal portion. A 70-year old female experienced paroxysmal and excruciating pain, starting in the right ear and descending to the tongue and throat. The pain was brief, burning and triggered by swallowing food and drinks. Preoperative CISS-MRI delineated a small vascular loop compressing the glossopharyngeal nerve at its cisternal portion. The patient was diagnosed with glossopharyngeal neuralgia, and then, microvascular decompression surgery was performed. Intraoperative inspection revealed that the glossopharyngeal nerve root was in contact with a small arterial loop at its cisternal portion and was deformed as demonstrated by preoperative CISS-MRI. The glossopharyngeal nerve was displaced using a piece of Teflon felt, freeing it from the arterial loop compression. The patient's neuralgia resolved immediately after surgery. During a period of 2-years follow up, no recurrence of the neuralgia has occurred. The usefulness of CISS-MRI for the diagnosis of glossopharyngeal neuralgia is discussed.