Small cell carcinoma usually involves the lung and rarely affects the biliary tract, especially the cystic duct. In this article we report a case of small cell carcinoma of the cystic duct in a 46-year-old Japanese man. The patient presented with abdominal pain and jaundice. Imaging showed a small nodule in the cystic duct invading the common bile duct with dilatation of the proximal biliary tree. The hepatic artery and portal vein were free from invasion. Extended right hepatic lobectomy, cholecystectomy, and resection of the extrahepatic proximal bile ducts were performed together with lymph node dissection under the tentative diagnosis of carcinoma of the cystic duct. Histopathologic examination of the resected specimen revealed small cell carcinoma arising in the cystic duct and extending into the common bile duct. The postoperative clinical course was uneventful, and the patient is doing well without any signs of recurrence 1 year after the operation. To our knowledge this is the first documented case of a small cell carcinoma arising in the cystic duct.