Objective: Report a rare case of a thyroid papillary carcinoma situated within a branchial cleft cyst. Case presentation: A 40-year-old male was referred to our department for a lateral neck mass assessment. Physical examination revealed a solitary palpable, painless, moveable neck mass. Assessment included complete nasal, pharynx and larynx endoscopy, neck computed tomography, and fine needle aspiration biopsy. Treatment was surgical excision of the neck mass. Histopathology confirmed a branchial cleft cyst with papillary thyroid carcinoma growth at a site. A neck and thyroid ultrasound showed presence of thyroid gland nodules (one of which with micro calcifications). Thyroid fine needle aspiration biopsy performed, was high suspicious for malignancy (BETHESDA V). Patient underwent total thyroidectomy and histopathology revealed papillary thyroid carcinoma. Conclusion: Although rarely, it is possible to face an unexpected malignancy within a clinically benign neck lesion. A thorough diagnostic work-up enables early identification of aforementioned potential malignancy. A diagnostic dilemma that arises in such cases is between primary or metastatic disease and a thyroid carcinoma arising from ectopic thyroid tissue.