Background and Aims: Although both per-oral endoscopic myotomy (POEM) and Heller myotomy (HM) have been used for the treatment of achalasia, the comparative efficacy of POEM and HM has yet to be fully evaluated. Methods: We searched all relevant studies published up to September 2018 examining the comparative efficacy between POEM and HM. Study quality was assessed using the Newcastle-Ottawa scale. Meta-analyses for Eckardt scores, perioperative outcomes, and reflux-related outcomes were performed based on a random-effects model. Results: Fifteen studies with a total of 1213 patients were evaluated. The follow-up duration ranged from 2 to 46.2 months and from 2 to 54.2 months in the POEM and HM groups, respectively. Postoperative Eckardt scores were lower (better) in the POEM group than in the HM group (pooled standardized mean difference [SMD], −0.58; 95% confidence interval [CI], −1.03 to −0.13). Length of myotomy was greater in the POEM group than in the HM group (pooled SMD, 0.63; 95% CI, 0.42-0.84). There was no difference in reflux symptoms and pathologic reflux on pH monitoring between the groups (pooled risk ratio [RR], 1.03; 95% CI, 0.61-1.73; and pooled RR, 1.22; 95% CI, 0.67-2.25, respectively). Erosive esophagitis on endoscopy tended to be less common in the HM group (pooled RR, 1.88; 95% CI, 0.98-3.62). Conclusion: Although long-term follow-up data are insufficient, the short-term efficacy of POEM was superior to that of HM. Erosive esophagitis tended to be more common in the POEM group; however, there was no difference in reflux symptoms and pathologic reflux on pH monitoring between the groups.