A 59-year-old woman was admitted to the hospital because of jaundice. Magnetic resonance cholangiopancreatography revealed dilation of the intrahepatic bile duct and obstruction at the bifurcation of the left and right hepatic bile ducts. An extended right lobectomy was performed under a suspected diagnosis of hilar cholangiocarcinoma. Histological diagnosis was sclerosing cholangitis characterized by periductal fibrosis with severe infiltration of chronic inflammatory cells. On hematological studies after the operation, antinuclear antibody test was positive and the serum IgG4 was elevated. Endoscopic retrograde pancreatography disclosed diffuse narrowing of the main pancreatic duct, and autoimmune pancreatitis was diagnosed. The patient's postoperative course was uneventful. We have to keep sclerosing cholangitis associated with autoimmune pancreatitis in mind as a differential dignosis of hilar cholangiocarcinoma.