We report a rare case of biliary papillomatosis arising in a congenital choledochal cyst, with an anomalous junction of the pancreatobiliary ductal system (AJPBDS). A 50-year-old woman was admitted to our department with epigastralgia, and imaging studies showed two masses in the cystic common bile duct and an AJPBDS. We made a preoperative diagnosis of biliary tract cancer, considering the size of the masses and the presence of the AJPBDS, and performed a pylorus-preserving pancreatoduodenectomy. The resected specimen contained two papillary tumors, which were subsequently diagnosed as benign papillomas. Histopathological and oncological examinations indicated that the lesions were involved in the development and progression of carcinogenesis because a point mutation of the K- ras gene and overexpression of p53 protein were detected. These findings suggest that biliary papillomatosis is a precancerous lesion induced by an AJPBDS.