Primary small cell thyroid carcinomas are extremely rare and there is still debate about their classification as a distinct disease entity. The present case report reports a small cell carcinoma (SCC) combined with poorly differentiated thyroid carcinoma (PDTC) in a 34 year old man. The tumor consisted of ~80% PDTC and ~20% SCC. The PDTC component was positive for cytokeratin and thyroid transcription factor-1 (TTF-1), and negative for calcitonin, chromogranin and synaptophysin. The SCC component was positive for synaptophysin and CD56, and negative for calcitonin, chromogranin and TTF-1. Seven months after thyroid surgery, two new lung nodules were detected. Histologically and immunohistochemically, the lung tumors were similar to the SCC component of the thyroid carcinoma. The mutational status of cancer-related genes was assessed using targeted next-generation sequencing in both the thyroid and lung, which identified similar genetic alterations. The histogenesis of SCC was evaluated through NGS analysis of the two cancer components.