BACKGROUND: Pancreaticobiliary maljunction (PBM) can be classified into two categories, PBM with congenital biliary dilatation (CBD) or PBM without biliary dilatation, and the management of PBM is often controversial. The treatment for PBM with CBD is prophylactic flow diversion surgery, and some authors have reported that the incidence of cancer after extrahepatic bile duct excision is less than 1%. A very rare case of intrahepatic cholangiocarcinoma 6 years after flow diversion surgery for PBM with CBD is reported. CASE SUMMARY: A 30-year-old man was diagnosed as having PBM with CBD, Todani classification type IVA, because of abnormal liver enzyme profiles. He underwent flow diversion surgery and cholecystectomy, and the specimen showed adenocarcinoma foci, pT1, pStage IA. Five and a half years passed without any recurrence of bile duct cancer. However, 6 years after his operation, computed tomography showed a gradually growing nodule in the bile duct. Fluorodeoxyglucose positron emission tomography showed high uptake, and magnetic resonance imaging showed restricted diffusion signals. On double balloon enteroscopy, the nodule at the posterior bile duct-jejunum anastomosis was directly visualized, and its biopsy specimen showed adenocarcinoma. The patient underwent right lobectomy and biliary reconstruction. The pathological diagnosis was intraductal papillary neoplasm with high-grade intraepithelial neoplasia, pTis, pN0, pStage 0. The patient's postoperative course was uneventful, and he has had no recurrence up to the present time. CONCLUSION: This case suggests the necessity of careful observation after flow diversion surgery, especially when PBM with CBD is detected in adulthood.