A 34-year-old female with papillary carcinoma of the thyroid originating in a thyroglossal cyst is described. The patient’s chief complaint was a submental mass. The mass was 6 × 4 cm, elastic, soft, and smooth-surfaced. CT examination showed high-density areas in part of the interior of the mass. Resection of the mass was attempted with a diagnosis of thyroglossal cyst. Since papillary carcinoma of the thyroid was noted in the cyst by intraoperative frozen section pathological examination, primary carcinoma of the thyroid was suspected, and the thyroid and surrounding areas were examined. Since no abnormalities were noted in the thyroid, the thyroid was preserved. According to the following reasons, the tumor was considered to be primary papillary carcinoma of the thyroid arising in the thyroglossal cyst: (1) Scar formation was noted in the center of the tumor; (2) tumor cells partly infiltrated into the surrounding tissues, and (3) no tumor was noted in the thyroid. A definitive diagnosis of carcinoma arising in the thyroglossal cyst has required confirmation of the absence of carcinoma in the thyroid by total thyroidectomy. In the present case, however, total thyroidectomy was avoided, because no gross pathological changes were observed in the thyroid during the operation. This decision may be controversial both diagnostically and therapeutically, but we consider from our observation of the course that total thyroidectomy is not always necessary.