Occurrence of malignancy in a thyroglossal duct cyst (TDC) in children and adolescents is very rare, preoperative diagnosis is a challenge, and appropriate management is still debated. We report a 19-year-old male patient referred for a midline neck mass diagnosed as an atypical TDC after initial and subsequent investigations. Ultrasound-guided fine-needle aspiration (FNA) of the mass was diagnostic for papillary thyroid carcinoma. Sistrunk procedure and total thyroidectomy were performed. Histologic analysis confirmed the presence of papillary thyroid carcinoma within TDC, infiltrating surrounding soft tissues. Postoperatively, radioiodine ablation treatment was administered, followed by TSH suppression therapy.