A rare autopsy case of primary squamous cell carcinoma of the thyroid gland is reported herein. A 61-year-old Japanese woman with a swelling of the left neck underwent surgery and the resulting tumor was histopathologically diagnosed as pure squamous cell carcinoma of the thyroid gland. She had had the nodule for 20 years, and it was histologically diagnosed as having been a well-encapsulated, follicular adenoma. Histopathological observation of the resected glands also revealed the coexistence of pure squamous cell carcinoma, which presumably originated from the adenoma. Postoperatively, an esophagotracheal fistula formed due to local invasion of the tumor cells. The patient’s state gradually deteriorated and she died of severe bronchopneumonia and renal dysfunction, 4 months after the operation. Autopsy revealed no distant metastases, but severe septicemia caused by bacterial infection affecting the systemic organs was found, which presemably resulted in multiple organ failure.