Congenital pyloric atresia (CPA) is a rare condition that presents as gastric outlet obstruction in the first few weeks of life. Isolated CPA typically carries a good prognosis but when associated with other conditions such as multiple intestinal atresia or epidermolysis bullosa (EB), the outcomes are generally poor. This report describes a four-day-old infant who presented with nonbilious emesis and weight loss in whom an upper gastrointestinal contrast study revealed gastric outlet obstruction determined to be consistent with pyloric atresia. The patient underwent operative repair via Heineke-Mikulicz pyloroplasty. Postoperatively, the patient continued to have severe diarrhea and was found to have desquamative enteropathy though had no skin findings consistent with EB. This report emphasizes consideration of CPA as a differential diagnosis for neonates presenting with nonbilious emesis and demonstrates the association between CPA and desquamative enteropathy without EB.