Small cell carcinoma of the bile duct system is extremely rare, and surgical procedures have been complicated by early hematogenous dissemination. In this study, we report a patient with small cell carcinoma of the bile duct system presenting with jaundice. The diagnosis was made early by endoscopic ultrasonography-guided fine needle aspiration biopsy (EUS-FNA). We performed radiation therapy of a total of 30 Gy, resulting in a marked decrease of serum neuron specific enolase levels and amelioration of jaundice, which had been resistant to drainage procedures. The patient was then treated with combined chemotherapy of cisplatin and CPT-11, which resulted in the disappearance of the tumor mass by image tests.