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Background Neoplasia of ectopic thyroid components is relatively rare in thyroglossal duct cysts. We report a case of histopathologically confirmed papillary thyroid carcinoma in a thyroglossal duct cyst, discuss its clinical characteristics of, and provide reference for diagnosis and treatment. Case Description We presented a 25-year-old female went to hospital because of “a tumor in her neck”. She was preoperatively diagnosed with thyroglossal duct cyst by cervical ultrasound, and enhanced computed tomography (CT). However, the solid component of the mass suggested intracystic neoplasia. She underwent Sistrunk surgical resection, and postoperative histopathology showed thyroglossal duct cyst, and papillary thyroid carcinoma in the cyst wall. The patient had no high-risk factors and had a low risk of recurrence. After full disclosure, the patient chose close follow-up, and to date there has been no recurrence. Conclusions There are controversies regarding the origin of thyroglossal duct cyst carcinoma and the extent of surgery required, and a lack of unified treatment guidelines. We recommend tailoring individualized treatment based on individual risk stratification. By reporting this case, we hope to inform surgeons of the various abnormalities that may occur in ectopic thyroid tissue.