We previously reported the case of a three-year-old patient with extrahepatic bile-duct cancer with congenital biliary dilatation (CBD), representing the youngest patient reported thus far with this disease. After surgery, a histopathologic examination confirmed well-differentiated adenocarcinoma with fibromuscular invasion and vascular infiltration, and the cut stump was positive for carcinoma -in-situ (CIS) at both the hepatic and distal margin of the bile duct. Since the patient was young, no additional therapy was selected after the surgery, and we have carefully followed the patient for more than 10 years with imaging and hematological examinations. To date, no abnormalities have been observed in his liver function, CA19-9 levels, or MRCP findings, and he has survived without recurrence for over 13 years since the surgery. A molecular biological reexamination of the initial resected specimen revealed that the cancer cells had no mutations in Kras codon 12, 13, 59, 61, 117, or 146 or Braf. The course of this case demonstrated the validity of surgery for pediatric biliary tract cancer associated with CBD. Furthermore, it was revealed that the positive resection margin in CIS of cholangiocarcinoma does not always recur even after a long period of time. However, the possibilities of late term recurrence of the disease and metachronous carcinogenesis at residual biliary tract still remain, so lifelong follow-up will be required for the patient.