Symptoms and complications of gastroesophageal reflux disease (GERD) following esophageal atresia (EA) repair are common and can persist beyond adolescence into adulthood. The sequelae attributed to GERD in this patient population include anastomotic stricture, dysphagia, esophagitis, and pulmonary complications. Prophylactic acid-suppressing medications, such as proton pump inhibitors (PPI), are commonly utilized following esophageal atresia repair with intent to decrease stricture formation and prevent respiratory sequelae of GERD; however, there is minimal evidence that prophylactic acid suppression prevents these complications, and no randomized trials exist to support this practice. Less evidence exists to support the continued use of acid suppression beyond infancy, with the long-term use of acid suppression following esophageal repair highly variable and primarily driven by symptomatology or presence of esophagitis on endoscopy. While anti-reflux procedures are frequently performed in those with refractory symptoms of GERD, outcomes following these operations in esophageal atresia patients are associated with increased morbidity and high failure rates. Therefore, anti-reflux operations should be pursued after failure of both medical and endoscopic management to control reflux or refractory strictures. Altogether, the management of GERD following esophageal atresia repair is a common and often complex problem, and few studies exist to provide guidance on the best approach.