Introduction This is a rare case of type II first branchial cleft cyst presenting as a congenital anomaly. The fistula extends from the front of the skin surface to the center of the sternocleidomastoid muscle. Case presentation A 2-year-old girl presented to pediatrician complaining of swelling and fluid discharge under her right ear for the past several months.The wound becomes infected, causing swelling and draining of fluid. Symptoms The child had difficulty swallowing, difficulty breathing, redness, and a rash. In examination Her vital signs were age appropriate. She had a right-sided, 1,5x1cm, round shaped, intense wound. Scar tissue around the wound. On Brain CT: Several <0.7cm lymph nodes in both neck LN stations. A diagnosis of Type II First Branchial Cleft Cyst was planned then Removal of type II first BCC was performed. There is no inter and post operative complications. Conclusion Treatment is complete surgical excision of all abnormally placed epithelium, while preserving surrounding neurovascular structures, and using cosmetically acceptable incisions.