Neuroendocrine carcinoma (NEC) in the extrahepatic bile duct is extremely rare and clinically aggressive. Cytological examination of bile and/or bile duct brushing specimens plays an important role in the diagnosis of carcinoma of the extrahepatic bile duct, but only a few articles have described the cytological features of NEC in this area. Thus, we retrospectively analyzed the cytological features of NEC in bile and/or bile duct brushing specimens. Patients with a histopathological diagnosis of NEC who underwent bile and/or bile duct brush cytological examination were enrolled in this study. The cytological features, including the background, arrangement, and shape of the neoplastic cells, and nuclear and cytoplasmic features were reviewed. Six patients with small cell NEC were enrolled, and two of them had pancreatic tumors directly invading the bile duct wall. The cytological specimens showed small and/or large neoplastic cell clusters with occasional single cells in all cases. The neoplastic cells had a high nuclear/cytoplasmic ratio and round‐to‐oval nuclei with powdery chromatin, inconspicuous nucleoli, and scant cytoplasm. Nuclear molding was a characteristic finding in all cases. One case had an adenocarcinoma component, which was also present in the cytological specimen. Cytological examination of bile and/or bile duct brushing specimens can be useful for the diagnosis of small cell NEC. This is an extremely rare but aggressive carcinoma, and its diagnosis by identifying characteristic cytological features may facilitate early detection and treatment.