Sclerosing cholangitis (SC) is one of the lesions frequently seen in IgG4-related systemic diseases, causing biliary stricture and mimicking bile duct carcinoma and primary sclerosing cholangitis (PSC). Although it often accompanies autoimmune pancreatitis (AIP), autoimmune-related SC without a pancreatic lesion is very rare. A 79-year-old woman was referred to our institution with suspected diagnosis of bile duct carcinoma in the previous hospital. The patient was not icteric and fever free, but with an elevated level of serum biliary enzyme, which lead us to detect this disease. Clinical images including computed tomography (CT), endoscopic retrograde cholangiopancreatography (ERCP) and intraductal ultrasonography (IDUS) demonstrated multiple strictures at the intrahepatic bile duct and enhanced wall thickness at the upper common bile duct, however her pancreas was normal. Repeated endoscopic procedures with multiple biopsies from the biliary strictures demonstrated fibrous ductal tissues with lymph-plasma cell infiltration (>10 IgG4(+) cells/HPF). By positron emission tomography using ¹⁸F-fluorodeoxyglucose (FDG-PET), the uptake of FDG was not remarkable in areas other than the biliary lesions. Additional laboratory tests showed elevated levels of serum IgG (2,571 mg/dL), and γ-globulin (29%), and positive autoantibodies, but normal IgG4 (53.2 mg/dL). Together with clinical images, laboratory and histological findings, we diagnosed this patient as sclerosing cholangitis which was thought to be associated with autoimmunity. After one year of follow-up without steroid therapy, idiopathic thrombocytopenic purpura (ITP) developed with an increased level of serological markers. We encountered a rare case of sclerosing cholangitis expected to be associated with autoimmunity, which showed biliary strictures mimicking bile duct carcinoma and needed careful diagnosis. Unlike the typical AIP, the current case demonstrated distinct serological findings and no other organ involvement. Further study is needed to clarify the characteristics of sclerosing cholangitis associated with autoimmunity with a large number of cases.