OBJECTIVE: The aim of this study was to compare the efficacy and safety of endoscopic microvascular decompression (E-MVD) and microscopic microvascular decompression (M-MVD) for the treatment for cranial nerve syndrome caused by vascular compression, including primary trigeminal neuralgia, hemifacial spasm, and glossopharyngeal neuralgia. METHODS: A systematic search of the online databases, including PubMed, Embase, Web of Science, Cochrane Central Register of Controlled Trials, China Biology Medicine disc, and China National Knowledge Infrastructure, was performed from January 1966 to March 2018. The language of the included literature was not limited. Relevant outcomes of perioperative safety and postoperative efficacy were considered for meta-analysis. Single-arm and cumulative meta-analyses were also conducted. All the outcomes were calculated as odds ratios (ORs) with 95% confidence intervals using R language. RESULTS: A total of 9 studies involving 1093 (E-MVD [543] vs. M-MVD [550]) patients were included for analysis in our study. The recent remission rate (92% vs. 86%; OR, 1.71; P = 0.0089), offending vessel discovery rate (99% vs. 95%; OR 2.76, P = 0.0061), and long-term remission rate (97% vs. 87%; OR 4.59, P = 0.0036) were significantly higher in patients who underwent E-MVD than in those who underwent M-MVD, whereas perioperative complications (23% vs. 35%; OR 0.56, P < 0.0001) were significantly lower in patients who underwent E-MVD. CONCLUSIONS: This meta-analysis confirms that E-MVD is superior to M-MVD both in perioperative and postoperative efficacy (short- and long-term), and therefore it should be considered as an appropriate treatment choice for patients with neuralgia and hemifacial spasm.