Objective To investigate the efficacy and safety of the microvascular decompression (MVD) for glossopharyngeal neuralgia (GN). Methods A systematic review was performed to retrieve relevant literatures up to February 2018 through PubMed, Embase and Web of Science database. The relevant literatures were screened according to the inclusion and exclusion criteria. The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) was used to conduct a quality evaluation for the included literatures. The relevant data were extracted to evaluate the immediate complete remission rate post operation, long-term remission, proportion of occurrence on the left side, proportion of posterior inferior cerebellar artery (PICA) as offending vessel, proportion of a single vessel as offending vessel, operational mortality and complications. Meta-analysis was conducted by using the meta package of R software. Results A total of 12 studies involving 665 patients were enrolled. The mean STROBE score of the included literatures was 16. The immediate complete remission after operation was achieved in 553 of 665 patients and the corresponding rate was 91% (95% CI: 83%-96%, I2=82%). The long-term remission was achieved in 298 of 335 patients and the corresponding rate was 87% (95% CI: 80%-93%, I2=64%). The symptoms of 387 in 665 patients were located on the left and the proportion of occurrence on the left side was 59% (95% CI: 52%-67%, I2=67%). The PICA was found to be the offending vessel in 292 of 408 patients and the corresponding proportion was 72% (95% CI: 68%-76%, I2=0). A single vessel was found to be the offending vessel in 336 of 408 patients and the corresponding proportion was 84% (95% CI: 77%-93%, I2=82%). The funnel plot and Egger linear regression demonstrated no publication bias. The cumulative meta-analysis suggested that the rate of remission did not change with a fixed trend with the date of the publication. Sensitivity analysis and subgroup analysis provided similar results. Conclusions The results of our meta-analysis suggested that MVD is an effective and safe modality of treatment for GN with high immediate postoperative complete remission rate, high long-term complete remission rate and low relapse rate. The surgical complications of MVD are few and slight, which is worth getting promoted. Key words: Glossopharyngeal neuralgia; Meta-analysis; Microvascular decompression; Efficacy; Safety