We present here the case of a 73-year-old man with squamous cell carcinoma that arose in a thymic cyst, and this was incidentally found by chest radiography. Computed tomography revealed a 3.6 cm-sized predominantly cystic lesion with a mural nodule at the antero-superior mediastinum. The resected specimen was a well demarcated cystic mass with a solid mural nodule. Microscopically, the nodule was determined to be invasive squamous cell carcinoma that had originated from the benign squamous epithelium lining the thymic cyst.