We report a case of cholangiocarcinoma with intestinal malrotation that was treated with pancreaticoduodenectomy. The patient was a 74-year-old man, who underwent laboratory screening and was subsequently found to have elevated γglutamyl transpeptidase levels. Preoperative ultrasonography revealed intrahepatic bile duct dilatation. Endoscopic retrograde cholangiopancreatography demonstrated a filling defect in the common bile duct and cytology of the bile demonstrated the presence of an adenocarcinoma. On preoperative computed tomography (CT), the SMV was located on the left side of the SMA, which showed the SMV rotation sign. Additionally, the small intestine and the colon were deviated to the right and left side of abdominal cavity, respectively. We diagnosed the patient with cholangiocarcinoma with intestinal malrotation and preduodenal portal vein involvement using the CT scan, and performed pancreaticoduodenectomy. Since the ligament of Treitz was absent during surgery, we diagnosed this as a case of the nonrotation type of malrotation. The postoperative course was uneventful and the patient was discharged from the hospital 42 days after the surgery. Anomalies of the portal venous system are so rare that recognition of its variation is important in order to avoid accidental injuries during the operation.