The endoscopist plays a critical role in the management of patients with congenital esophageal defects. This review focuses on esophageal atresia and congenital esophageal strictures and, in particular, the endoscopic management of comorbidities related to these conditions, including anastomotic strictures, tracheoesophageal fistulas, esophageal perforations, and esophagitis surveillance. Practical aspects of endoscopic techniques for stricture management are reviewed including dilation, intralesional steroid injection, stenting, and endoscopic incisional therapy. Endoscopic surveillance for mucosal pathology is essential in this population, as patients are at high risk of esophagitis and its late complications such as Barrett’s esophagus.