We report a neonatal case of “intraluminal” pyloric duplication cyst, causing gastric obstruction after birth. Endoscopy revealed a submucosal cystic lesion approximately 15 mm in size arising from the anterior and inferior surfaces of the pylorus obliterating the pyloric canal. After laparotomy, intraoperative cholangiography was performed, which documented no communication between the cyst and the bilio-pancreatic duct. Gastrotomy was performed transversally over the antrum, and the cyst delivered through the incision. The cyst was incised, the upper part of the cyst wall removed, and a mucosectomy performed on the inner cyst wall of the lower part. The mucosa and muscle of the margin of the cyst were approximated. At follow up of 10 months, the patient is well without any sign of gastric obstruction.