Thyroglossal duct cysts (TDC) are the most common congenital anomalies of the thyroid gland and less than 1% of them become malignant. The malignancy most often found is papillary carcinoma. The diagnosis is usually made postoperatively. Controversy exists whether TDC are primary or secondary and also as for their treatment regime. In this case report, we present a 30-year-old woman with papillary carcinoma of the TDC, identified only by pathology after surgical ablation by Sistrunk's procedure. Invasion of the carcinoma to the adjacent tissues or lymph node metastases were not found. Thyroid function tests were normal as well as the thyroid scan. After a two-year follow up, the patient remained asymptomatic with no evidence of recurrence, as tested clinically and by ultrasonography. Since our patient had no marginal invasion of the carcinoma in the surrounding tissues or lymph node metastases, we recommended the Sistrunk's surgical procedure, suppressive treatment by thyroid hormones and long term follow-up.