To date very few studies with small sample size have compared peroral esophageal myotomy (POEM) with the current surgical standard of care, laparoscopic Heller myotomy (LHM), in terms of efficacy and safety, and no recommendations have been proposed. To investigate the efficacy and safety of POEM compared with LHM, for the treatment of achalasia. The databases of Pubmed, Medline, Cochrane, and Ovid were systematically searched between January 1, 2005 and January 31, 2015, with the medical subject headings (MeSH) and keywords “achalasia,” “POEM,” “per oral endoscopic myotomy,” and “peroral endoscopic myotomy,” “laparoscopic Heller myotomy” (LHM), “Heller myotomy.” All types of study designs including adult patients with diagnosis of achalasia were selected. Studies that did not report the comparison between endoscopic and surgical treatment, experimental studies in animal models, single case reports, technical reports, reviews, abstracts, and editorials were excluded. The total number of included patients was 486 (196 in POEM group and 290 in LHM group). There were no differences between POEM and LHM in reduction in Eckardt score (MD = −0.659, 95% CI: −1.70 to 0.38, P = 0.217), operative time (MD = −0.354, 95% CI: −1.12 to 0.41, P = 0.36), postoperative pain scores (MD = −1.86, 95% CI: −5.17 to 1.44, P = 0.268), analgesic requirements (MD = −0.74, 95% CI: −2.65 to 1.16, P = 0.445), and complications (OR = 1.11, 95% CI: 0.5–2.44, P = 0.796). Length of hospital stay was significantly lower for POEM (MD = −0.629, 95% CI: −1.256 to −0.002, P = 0.049). There was a trend toward significant reduction in symptomatic gastroesophageal reflux rate in favors of LHM compared to POEM group (OR = 1.81, 95% CI: 1.11–2.95, P = 0.017). All included studied were not randomized. Furthermore all selected studies did not report the results of follow-up longer than 1 year and most of them included patients who were both treatment naive and underwent previous endoscopic or surgical interventions for achalasia. POEM represents a safe and efficacy procedure comparable to the safety profile of LHM for achalasia at a short-term follow-up. Long-term clinical trials are urgently needed.