The thyroglossal duct cysts (TGDCs) are the most common congenital anomaly of the thyroid, usually manifested as painless midline neck mass. Malignancy is very rare and is reported in around 1% of cases as an incidental finding after histopathological evaluation of resected cyst. Papillary carcinoma is the most common carcinoma reported in TGDC. Here, we report a case of 17-year-old-female, who presented with a gradually increasing midline neck mass which moves with swallowing. On imaging a diagnosis of infected TGDC was made. The Sistrunk operation was done and a diagnosis of primary papillary carcinoma arising in a TGDC was rendered histopathologically. The contemporary appearance of papillary carcinoma thyroid was reported in about 20% cases of TGDC carcinoma, thus it is essential to differentiate primary papillary carcinoma arising in a TGDC from those of metastatic papillary carcinoma thyroid by strict diagnostic criteria.