Eosinophilic esophagitis is an immune-mediated chronic disease of the esophagus characterized by symptoms related to esophageal dysfunction and tissue eosinophilia. In the endoscopy, the esophageal mucosa may appear normal or show exudates, rings, edema, furrows, and strictures. Its management is based on elimination diet, topical corticosteroids and/or esophageal dilation. Atresia is the most common congenital alteration of the esophagus; it requires surgical repair and poses potential complications, such as gastroesophageal reflux, strictures, and esophageal dysmotility. Up to 2015, 48 cases of eosinophilic esophagitis and esophageal atresia were reported, with dysmotility, reflux, and long-term acid suppression involvement. Prevalent clinical signs include dysphagia, difficulty eating, and reflux symptoms, so an esophagogastroduodenoscopy with biopsy is recommended to rule out associated eosinophilic esophagitis in patients with esophageal atresia and persistent symptoms before performing an esophageal dilation and/or anti-reflux surgery. If eosinophilic esophagitis is confirmed, it should be managed with the corresponding drugs, and the subsequent therapeutic approach will depend on its clinical course.