Cysts arising from the lateral neck commonly represent benign lesions such as branchial cysts and lymphangiomas. Occasionally a cyst of the lateral cervical region is a malignant lesion metastatic from a papillary thyroid carcinoma. Ectopic thyroid tissue within a branchial cleft cyst may present as an exceptional finding: a primary thyroid carcinoma. Here we a report a rare case of ectopic thyroid papillary carcinoma that presented as lateral neck cyst with preoperative diagnosis of branchial cleft cyst. After complete surgical resection and histopathologic examination, the lesion was determined to be a branchial cleft cyst with primary thyroid papillary carcinoma.