Peroral endoscopic myotomy (POEM) and Heller myotomy with fundoplication (HMF) effectively treat achalasia, an esophageal motor disease. Although a significant number of meta-analyses have compared POEM and HMF, these studies showed discrepant postoperative gastroesophageal reflux disease (GERD) conclusions. This review aimed to objectively compare GERD over time, as well as the efficiency, safety, and adverse events in POEM versus HMF for treating achalasia.We performed a systematic review and meta-analysis by searching Medline, Embase, Cochrane Library, Scopus, and Clinicaltrials.gov. The evaluated outcomes included early (within 12 months) and late (beyond 12 months) endoscopic assessment of GERD using the Lyon Consensus, clinical success, operative duration (OD), length of stay (LOS), and major adverse events (MAE).A total of 29 observational studies and two randomized clinical trials (RCTs) with 13,914 patients were included. GERD was 28% higher among RCTs discussing POEM at early assessment (95%CI 0.02, 0.54) and was not different at late evaluation (95% confidence interval (CI) = 0.00, 0.22). No difference in reflux was observed among observational studies in both periods. The clinical success was 9% higher (95% CI = 0.05, 0.12), and the OD was 37.74 minutes shorter (95% CI = -55.44, -20.04) in POEM among observational studies, whereas it was not different among RCTs. The LOS and MAE were similar in the groups.Comparisons among studies yielded divergent results. RCTs revealed that POEM had a higher incidence of GERD in the early assessment, whereas observational studies showed higher clinical success and a shorter OD in POEM. Ultimately, the between-group difference waned over time in GERD in all comparisons, resulting in no difference among RCTs in the late evaluation. Our meta-analysis demonstrated a nonpreferential treatment of achalasia between endoscopic or surgical cardiomyotomy, prioritizing an individualized approach in the long term.