Abstract Introduction Thyroglossal duct cyst (TGDC) is themost common congenital anomaly of the neck, and approximately 7% of all the adult population presents it. Ectopic thyroid tissue is found in the thyroglossal duct cyst wall in up to 65% of cases. This thyroid tissue has the potential to develop some type ofmalignancy, themost common of which is the papillary carcinoma of the thyroid. There are just over 270 cases of thyroglossal duct cyst malignancy reported in the literature. Objectives We aimed to study our population of patients in order to identify cases with thyroglossal duct cyst malignancy. Methods A retrospective chart review was conducted in the section of otolaryngology/ head and neck surgery at a hospital in Karachi, Pakistan, from January of 2004 to December of 2014 on patients with the diagnosis of thyroglossal duct cyst. Results Fifty-eight patients were diagnosed with TGDC, two of whom also presented with thyroglossal duct cyst carcinoma. Both patients revealed papillary thyroid carcinoma on histopathology. Case 1 had an open biopsy before undergoing definitive surgery. Both patients underwent subsequent total thyroidectomy after Sistrunk procedure, and case 2 had selective neck dissection revealing lymph node metastasis. Conclusion Thyroglossal duct cyst carcinoma is a rare finding that comes as a surprise to both the patient and the surgeon. We report 2 out of 58 cases diagnosed with thyroglossal duct cyst carcinoma.