A case of thyroid papillary carcinoma arising in ectopic thyroid tissue within a branchial cleft cyst is described. Complete dissection of the thyroid gland was necessary to rule out the differential diagnosis of primary thyroid carcinoma. The thyroglossal duct tract is an unusual localization for thyroid carcinomas in ectopic thyroid tissue. Thyroid carcinoma arising in ectopic thyroid tissue within a branchial cyst is extremely rare. Complete thyroidectomy may be necessary to eliminate an occult thyroid carcinoma.