Introduction Many centers have reported excellent short-term efficacy of per-oral endoscopic myotomy (POEM) for the treatment of achalasia. However, long-term data are limited and there are few studies comparing the efficacy of POEM versus Heller Myotomy (HM). Aims To compare the long-term clinical efficacy of POEM versus HM. Methods Using a retrospective, parallel cohort design, all cases of POEM or HM for achalasia between 2010 and 2015 were assessed. Clinical failure was defined as (a) Eckardt Score > 3 for at least 4 weeks, (b) achalasia-related hospitalization, or (c) repeat intervention. All index manometries were classified via Chicago Classification v3. Pre-procedural clinical, manometric, radiographic data, and procedural data were reviewed. Results 98 patients were identified (55 POEM, 43 Heller) with mean follow-up of 3.94 years, and 5.44 years, respectively. 83.7% of HM patients underwent associated anti-reflux wrap (Toupet or Dor). Baseline clinical, demographic, radiographic, and manometric data were similar between the groups. There was no statistical difference in overall long-term success (POEM 72.7%, HM 65.1% p  = 0.417, although higher rates of success were seen in Type III Achalasia in POEM vs Heller (53.3% vs 44.4%, p  < 0.05). Type III Achalasia was the only variable associated with failure on a univariate COX analysis and no covariants were identified on a multivariate Cox regression. There was no statistical difference in GERD symptoms, esophagitis, or major procedural complications. Conclusion POEM and HM have similar long-term (4-year) efficacy with similar adverse event and reflux rates. POEM was associated with greater efficacy in Type III Achalasia.