Branchial remnant cysts are an uncommon cause of masses of the throatlatch area in horses. Two methods of treatment have been proposed in literature, both with complications. This manuscript proposes a method (marsupialization and sclerotherapy) for the treatment of a cyst in a 1.5-year-old Arabian filly. Diagnosis was made by ultrasonographic, radiographic and endoscopic examinations, revealing an anechoic fluid-filled structure and a well-defined capsule not in communication with other structures. After emptying the cyst, the skin was sutured circumferentially to the cyst wall; it was then flushed first with a solution of ethanol and povidone-iodine, then with sterile saline. Eight months after surgery, the filly had no recurrence of the cyst and the stoma was healed.