The report presents a rare case of carcinoid tumor in a 17 year female who presented with epigastric pain of one week duration. She was diagnosed to have type I choledochal cyst on abdominal ultrasound and MRI. She underwent total excision of choledochal cyst with roux-en-Y hepaticojejunostomy. Histopathological examination revealed a neuroendocrine tumor within choledochal cyst which was immunoreactive for Chromogranin A. Patient is well at 6 months of follow up. These tumors are characteristically slow-growing, therefore awareness of its presence preoperatively can facilitate optimal management by performing surgical resection with negative margins which offers the best chance of long-term survival.