Metastatic intrathyroid thymic carcinoma (ITTC) is a rare cancer that has no effective drugs. Herein, we report that comprehensive cancer mutation analysis revealed amplification of CD274 gene encoding PD-L1. Multiplex immunohistochemistry also clarified the presence of an immunosuppressive microenvironment via a PD-1/PD-L1 pathway in metastatic ITTC.