Background A 21 day old male child presented with non bilious vomiting and abdominal mass. Case presentation This case is reported because pyloroduodenal duplication cysts are an extremely rare congenital anomaly, whose clinical presentation often mimics those of hypertrophic pyloric stenosis. Ultrasound examination showed cystic mass at pyloric region and barium study was suggestive of extrinsic mass compressing the pyloric region. A laparotomy, a tense cystic mass was present at the pyloroduodenal junction (PDC) which was resected and end to end anastomosis was done. Patients followed an uneventful recovery and doing well. Conclusion The clinical and radiological analysis can reveal configurational changes consistent with a large extrinsic mass rather than muscular hypertrophy and can lead to accurate preoperative diagnosis.