Abstract Background Patients with preoperative ineffective esophageal motility (IEM) are thought to be at increased risk for postoperative dysphagia leading to the recommendations for tailoring or avoiding anti-reflux surgery in these patients. The aim of this study was to evaluate if IEM has an influence on postoperative outcome after laparoscopic Nissen fundoplication (LNF). Methods Seventy-two consecutive patients with IEM underwent LNF and were case-matched with 72 patients without IEM based on sex, age, BMI, HH size, total pH percentage time, total number of reflux episodes and the presence of BE. Standardized interview assessing postoperative gastrointestinal symptoms, proton pump inhibitor intake, GERD-health-related-quality-of-life (GERD-HRQL), alimentary satisfaction and patients’ overall satisfaction was evaluated. Results Although a higher rate of preoperative dysphagia was observed in patients with IEM (29% IEM vs. 11% no IEM, p = 0.007), there was no significant difference in rates of dysphagia postoperatively (2 IEM vs. 1 no IEM, p = 0.559). Furthermore, no distinction was found in the postoperative outcome regarding symptom relief, quality of life, gas bloating syndrome, ability to belch and/or vomit or revision surgery between the two groups. Conclusion Although preoperative IEM has an influence on GERD presentation, it has no effect on postoperative outcome after LNF. IEM should not be a cause for avoiding LNF, as is has been shown as the most effective and safe anti-reflux treatment.