One of the main reasons to resect choledochal cyst (CC) is to prevent malignant transformation. After resection of CC, the remnant intrapancreatic bile duct is no longer exposed to the enzymatic insult from pancreatic juice activated by the bile. Thus theoretically, the risk of malignant transformation disappears. We present a case showing development of adenocarcinoma from the remnant CC 16 years after resection of CC. A 43 year-old female patient underwent resection of type I CC 16 years ago, leaving a small remnant portion of CC as it was located deep within the pancreas close to the anomalous union of the pancreatobiliary duct. Four years later, intrahepatic ducts were dilated due to anastomotic stricture of the hepaticojejunostomy, which was resolved after repeated balloon dilatation. On follow-up examination at postoperative 16 years, a mass within the pancreas head was identified. As the mass was identified as adenocarcinoma on biopsy, pylorus-preserving pancreatoduodenectomy was performed. Pathologic examination showed a 3.5 cm-sized moderately differentiated adenocarcinoma arising from the remnant CC, with no lymph node metastasis. The patient recovered uneventfully, and is currently undergoing adjuvant chemotherapy. This case indicates that remnant CC can undergo malignant transformation. Therefore, complete resection of CC coupled with life-long follow-up is emphasized.