Patients with esophageal atresia (EA) suffer from abnormal and permanent esophageal intrinsic and extrinsic innervation that affects severely esophageal motility. The repair of EA also results in esophageal shortening that affects distal esophageal sphincter mechanism. Consequently, gastroesophageal reflux (GER) is common in these patients, overall approximately half of them suffer from symptomatic reflux. GER in EA patients often resists medical therapy and anti-reflux surgery in the form of fundoplication is required. In patients with pure and long gap EA, the barrier mechanisms against reflux are even more damaged, therefore, most of these patients undergo fundoplication during first year of life. Other indications for anti-reflux surgery include recalcitrant anastomotic stenoses and apparent life-threatening episodes. In short term, fundoplication alleviates symptoms in most patients but recurrences are common occurring in at least one third of the patients. Patients with fundoplication wrap failure often require redo surgery, which may be complicated and associated with significant morbidity. A safe option in a subset of patients with failed anti-reflux surgery appears to be long-term medical treatment with proton pump inhibitors.