Background: Safer and minimal invasive treatment options with minor side effects are in great demand in the treatment of glossopharyngeal neuralgia (GPN). Pulsed radiofrequency (PRF) is a micro-destructive procedure that could be applied repeatedly without irreversible damage to target tissue. However, few studies have reported the long-term clinical outcomes of PRF in the management of idiopathic GPN patients. Methods: We retrospectively investigated the efficacy and safety of computed tomography (CT)-guided PRF in the treatment of 30 patients with idiopathic GPN in a multi-center clinical study. Numeric rating scale (NRS) score was used to evaluate pain intensity before and after PRF treatment. The effective rate was defined as the percentage of patients with NRS reduction of more than 50%. Baseline characteristics, surgical records, initial pain relief, time to take effect, long-term outcomes, patient satisfaction using a five-level Likert Scale, the incidence of recurrence as well as subsequent treatment choices, intraoperative and postoperative complications were retrieved from electronic medical records. Results: A total of 30 idiopathic GPN patients who received PRF under CT-guidance were included in our study and the initial effective rate was 93.3%. The cumulative proportion of patients with satisfactory pain relief survival was 93.3% at 12 months, 89.6% at 24 months, 85.3% at 36 months, 79.6% at 48 months, 73.0% at 60 months and 72 months, and 54.8% at 84 months, 108 months as well as 120 months. No serious morbidity or mortality were observed in any of the cases. The median patient satisfaction in Likert scale rating was 4.0 (IQR, 3.0–5.0). Conclusion: According to our results, PRF is an effective and safe therapy for patients with idiopathic GPN. This minimally invasive, micro-destructive, neuro-modulatory technique could be a potential intervention of choice for the treatment of GPN patients who respond poorly to pharmacological treatment. © 2020 Jia et al.