We report a case of type-B3 thymoma manifesting neuroendocrine differentiation. The patient was a 42-year-old woman who complained of shoulder pain but had no symptoms of myasthenia gravis or anemia. The tumor was located in the anterior mediastinum and had directly invaded the pericardium and left lung. Histological examination revealed that the tumor was lobulated by bands of fibrous tissue, perivascular spaces were scattered throughout the tumor, and there were a few intraepithelial lymphocytes. The vast majority of lymphocytes in the perivascular spaces and in the lobulated tumor were immunohistochemically positive for TdT, MIC2, and CD1a. The majority of tumor cells were polygonal and medium or large in size. The tumor cells were weakly positive for synaptophysin, chromogranin A, CD56, and NSE. Small nests of small, relatively uniform polygonal cells were observed facing the fibrous bands. These cells resembled the cells of carcinoid tumors and were strongly positive for NSE, synaptophysin, chromogranin A, and CD56. Ultrastructurally, sparse dense-core granules were observed in the cytoplasm of a few tumor cells. This is a unique case of thymoma with neuroendocrine differentiation, and to the best of our knowledge this is the first such case ever reported.