Airway obstruction is a severe life-threatening perioperative complication of orthodontic surgery. Although hemorrhage and swelling are common after surgery, they are rarely caused by congenital and developmental anomalies of the airway. In the present study, we conducted orthodontic surgery on a patient with first and second branchial arch syndrome associated with bilateral cleft lip, who subsequently developed airway obstruction that might have been caused by an airway malformation. The patient was a 28-year-old male for whom orthodontic surgery for marked mandibular deviation was planned. Surgery involved corticotomy of the anterior maxillary alveolar region and sagittal split ramus osteotomy. After surgery and upon removal of the endotracheal tube, the subject developed wheezing and cyanosis, and so emergency tracheotomy was performed. However, in addition to the airway malformation, left deviation was observed, which made it difficult to clearly visualize the airway. Furthermore, the tracheal cartilage was fragile and easily deformed due to pressure of the flat trachea. After clearly visualizing the airway, an incision was made using a scalpel, which was very easy to perform, similar to making an incision along a blood vessel wall. Tracheomalacia has been described as a possible congenital complication of first and second branchial arch syndrome and the findings in the present case suggest that acquired tracheomalacia was the etiology. In future, after assessing any combined malformations, thorough preoperative evaluations including the airway should be conducted, and preventive tracheotomy should be performed as a postoperative management scheme when necessary, with the consent of the patient.