Intraductal papillary neoplasm of the bile duct (IPNB) is a variant type of the bile duct carcinoma characterized by intraductal growth. IPNB is also recognized as a precursor of invasive carcinoma. We describe herein an extremely rare case of IPNB arising from the cystic duct. A 68-year-old man was admitted to our hospital for investigation of epigastralgia and abnormal levels of biliary tract enzyme. Computed tomography and magnetic resonance imaging showed a mass lesion spreading from the cystic duct to the upper-middle bile duct. Endoscopic retrograde cholangiography demonstrated diffuse duct dilation with a grossly visible intraductal mass and amorphous blobs, suggesting the presence of mucobilia or scattered tumors. We performed extrahepatic bile duct resection with lymphadenectomy. Macroscopically, a friable papillary tumor originated from the cystic duct grows intraluminally into the bile duct. Pathologically, the tumor was found to be intramucosal adenocarcinoma spreading to the whole extrahepatic bile duct, which was compatible with IPNB. We should discuss the features and progression processes of IPNB through this precious case.