Branchial cleft cysts are the most common lesions to arise laterally in the neck. Ectopic thyroid tissue within a branchial cleft cyst is rare, and a papillary carcinoma arising from this tissue is extremely rare. We present a case of a lateral neck cyst representing a primary papillary carcinoma that arose in ectopic thyroid tissue within a branchial cleft cyst in a 41-year-old woman. After the mass was surgically excised, thyroid ultrasonography, thyroid scintigraphy, and whole-body F18-fluorodeoxyglucose-positron emission tomography/computed tomography detected no abnormality. The negative findings notwithstanding, surgery on the thyroid gland was planned, but the patient refused it. Therefore, she was followed up with ultrasonography and scintigraphy for 5 years, during which time she exhibited no evidence of recurrence. Total thyroidectomy is still the primary option in such cases, but when it cannot be performed for any reason, vigilant follow-up is essential.