Background and aimThe incidence of gastroesophageal reflux disease (GERD) is high after per‐oral endoscopic myotomy (POEM). GERD after POEM may be qualitatively different from GERD in patients without motility disorders. In this study, we aimed to analyze and compare different aspects of GERD between patients with post‐POEM GERD and nonachalasia GERD.MethodsThe data of patients with GERD after POEM (January 2018 to June 2019) were compared with that of a control group (nonachalasia GERD group), which included patients presenting with typical reflux symptoms without associated major motility disorders. Patients with lower esophageal sphincter pressure lower than 10 mmHg were excluded from the study. GERD was evaluated at 3 months after POEM. Esophageal acid exposure time higher than 4.2% was used to define GERD. The primary outcome of the study was comparison of GERD‐related quality of life and reflux symptom severity between the two groups. In addition, the severity of erosive esophagitis and reflux‐symptom association were also recorded in the two groups.ResultsA total of 100 patients were included in the study, with 50 patients in each group (post‐POEM GERD vs. controls). The baseline parameters were comparable between the two groups. Median interquartile range of GERD‐related quality of life score was significantly lower in the post‐POEM group (11 [0–23.3] versus 34 [24–44]; p < 0.001). The post‐POEM GERD group had significantly lower median heartburn (6.0 [0–16.3] versus 15.5 [7.5–24.8]; p = 0.001) and regurgitation scores (0 [0–6.0] versus 20.0 [12.3–25.0]; p < 0.001). Erosive esophagitis was more frequent in the post‐POEM group (28 [56%] versus 10 [20.4%], p = 0.001). Only three (6%) patients in the post‐POEM group had a positive reflux‐symptom association as compared with 28 (56%) patients in the control group (p < 0.001).ConclusionIn selected patients with pH positive GERD after POEM, the symptoms are milder and reflux‐symptom association is poor in spite of more severe esophagitis as compared with controls.