Ectopic thyroid tissue occurs in about 1 in 10,000 people. It can be seen anywhere from foramen caecum to lower neck region. But, it is rarely seen in a lateral neck mass, especially in branchial cleft cyst. Transformation to a malignant state in an ectopic thyroid tissue is uncommon, with most of the diagnoses found routinely through the post-operative histopathological analysis. Hereby, we report a rare case of an ectopic papillary thyroid carcinoma with an initial pre-operative diagnosis of a branchial cleft cyst. However, no primary thyroid gland malignancy was found. The pathophysiology and rarity of these disorders are explored. A high index of suspicion of ectopic tissue and malignancy must be in mind while attending to patients with long-standing, uninvestigated lateral neck masses. Excision biopsy and histopathological study are the two definitive steps to be undertaken