Third branchial cleft anomalies are rare congenital abnormalities with a complicated anatomical course. The traditional standard of treatment is complete open excision of the entire tract, but newer endoscopic and combined approaches are becoming more common. We summarize the anatomy, presentation, and evaluation of these anomalies. A review of the literature regarding the various surgical options and their associated risks and benefits is discussed. We then review the details of open excision, endoscopic treatment, and combined open or endoscopic surgical options. Given the higher risk of complications with open excision and the similar rates of recurrence with open and endoscopic procedures, we recommend endoscopic management of third branchial cleft anomalies as the first-line treatment.