Intrahepatic cholangiocarcinoma (ICC) is one of the life-threatening complications of primary sclerosing cholangitis (PSC). However, the incidence of ICC in Japanese PSC patients is low, and the association between the development of ICC and morbidity duration of PSC is largely unknown. Here, we describe a case of ICC that developed after a long-term follow-up of a patient with PSC and ulcerative colitis (UC). At the age of 10 years, the patient was first diagnosed with UC and its remission was achieved with systemic steroid therapy. Since then, he was routinely followed-up. At the age of 19 years, laboratory tests showed abnormalities in liver function parameters, and the patient was diagnosed with PSC. Although treatment with ursodeoxycholic acid improved the abnormalities in serum levels of biliary enzymes and no PSC-related symptoms were seen for 13 years, calculous cholecystitis frequently occurred in the patient since the age of 32 years. He developed ICC, which expressed some hepatic progenitor cell markers such as CD133, neural cell adhesion molecule, keratin 7, and keratin 19 at the age of 33 years. ICC was treated by curative partial hepatectomy and adjuvant chemotherapy with gemcitabine. Eight months later, however, the patient developed multiple metastases in the abdominal lymph nodes and lungs, and died 21 months after the onset of ICC. Here, we report a case of ICC that developed after a 14-year follow-up of a patient with PSC and UC.