Thymomas are tumors originating from the thymus epithelial cells and are the most common tumors of the anterior mediastinum. They have been classified into types A, AB, B1, B2, and B3 by the World Health Organization. Type B3 thymoma is composed of epithelial cell sheets with mild to moderate atypia and scant lymphocytes. An association between thymic carcinoma and neuroendocrine differentiation has been observed by some authors. However, cases of type B3 thymoma with neuroendocrine differentiation are very rarely discussed in the literature. A 68-year-old woman was referred to our hospital with an abnormal shadow on a chest roentgenogram. Chest computed tomography showed that the lesion was located in the anterior mediastinum. She underwent surgery, and the tumor was diagnosed as a type B3 thymoma with neuroendocrine differentiation. An extremely rare case of a type B3 thymoma showing neuroendocrine differentiation is presented herein.