Introduction Heller myotomy (HM) remains the gold standard procedure for achalasia. The addition of different types of fundoplication to HM has been debated in several studies. Given the contradictory reports, this meta-analysis was undertaken to compare different outcomes after HM and HM with fundoplication (HMF). Methods An electronic search was performed among five major databases (PubMed, Ovid, Scopus, Cochrane Library, Google Scholar) from inception to October 2019, identifying all randomised and non-randomised studies comparing HM with HMF. Two authors searched electronic databases using the keywords ‘achalasia’ AND ‘dysphagia’ AND ‘gastroesophageal reflux’ and all data were pooled for random-effects meta-analysis. The primary and secondary outcomes were gastroesophageal reflux and dysphagia, respectively. Results A total of six studies were included and involved 576 patients comparing HM and HMF. There was no statistically significant difference between gastroesophageal reflux in the HM vs HMF group (21.3% vs 22.9%, RR 1.32, 95% CI 0.60–2.88, p = 0.49). There was a slightly higher incidence of dysphagia observed in HM vs HMF (14.8% vs 10.8%, RR 1.54, 95% CI 0.98–2.41, p = 0.06). Conclusions There was no statistically significant difference in long-term outcomes between a group of patients undergoing HM and a group who underwent HM with fundoplication.