The more severe forms of laryngotracheal clefts — grades 3 and 4 — must be surgically repaired through an open incision in the neck to perform a double-layer closure of the defect. This may be done on either extracorporeal membrane oxygenation (ECMO) or cardiopulmonary bypass depending on the child's condition and the surgeon's preference.

The major purpose of the surgical repair is to separate the child's airway from his esophagus in order to prevent aspiration. This occasionally requires the placement of a tracheostomy tube to provide a safe airway for the child.