Background Gastroesophageal reflux disease (GERD) is a common disease in children. When drug treatment fails, laparoscopic anti-reflux surgery (LARS) is considered. Short-term follow-up studies report high success rates; however, few studies report long-term results. The aim of this study was to describe the long-term effects of LARS in pediatric patients. Methods A prospective, multicenter study of 25 laparoscopic fundoplication patients was performed. At 3 months and 1, 2, and 5 years postoperatively, patients and caregivers were asked to complete the gastroesophageal reflux symptom questionnaire to assess symptoms and the PedsQL™ to assess health-related quality of life (HRQoL). Results Reflux symptom severity was still significantly improved 5 years after LARS compared with preoperative levels (p < 0.0001). However, 26% of patients reported moderate or severe reflux symptoms. Dysphagia was reported in 13% of patients 5 years after LARS and was more common in children with neurologic impairment and children who underwent a Nissen procedure. The increase in HRQoL 3 months postoperatively appears to decline over time: 5 years after surgery, HRQoL was lower, though not significantly, than 3 months postoperatively. HRQoL at 5 years was still higher, though also not significantly, than preoperative levels. The presence of reflux symptoms after surgery was not significantly associated with lower HRQoL. Conclusions LARS is effective for therapy-resistant GERD in children. Five years after surgery, reflux symptoms are still improved. However, we observed a decline in symptom-free patients over time. The initial increase in HRQoL shortly after LARS appears to decline over time. Trial Registration Dutch national trial registry Identifier: 2934 (www.trialregister.nl)