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Abstract Objectives This study aimed to investigate the differences in the effectiveness of percutaneous radiofrequency thermocoagulation (PRT) and microvascular decompression (MVD) in treating glossopharyngeal neuralgia (GPN). Methods Medical records of patients were reviewed to investigate their baseline characteristics and immediate postoperative prognosis. Long-term outcomes of these patients were obtained through telephone interviews. Visual analog scale (VAS) and Pittsburgh sleep quality index (PSQI) scores at 1 day and 1, 4, 12, 24, and 48 weeks after surgery were compared between the MVD and PRT groups, in addition to complete pain relief rate, effective rate, adverse reactions, length of hospital stay, and economic indicators. Results The VAS and PSQI scores of the two groups at 1 day and 1, 4, 12, 24, and 48 weeks after surgery were significantly lower (P |