Papillary carcinoma arising in the branchial cleft cyst(BCC) is extremely rare and it generally results from metastasis of thyroid carcinoma. Primary papillary carcinoma arising in the branchial cleft cyst is more extremely rare and it develops without any evidence of a papillary carcinoma in thyroid gland. Here we report a 42 year-old man with papillary carcinoma originating from a branchial cleft cyst on the right lateral neck. The patient underwent simply excision of branchial cleft cyst and papillary carcinoma was identified incidentally after surgery. We then evaluate the thyroid gland for co-existing a papillary carcinoma in the thyroid gland, but absolutely no malignancy in the thyroid gland. We followed up to 6 years after surgery. Although not enough follow-up period, this report suggests that a papillary carcinoma in the BCC could be developed primarily in the ectopic thyroid tissues existing within the BCC.