Emanuel syndrome is associated with supernumerary chromosome, which consists of the extra genetic material from chromosome 11 and 22. The frequency of this syndrome has been reported as 1 in 110,000. It is a rare anomaly associated with multiple systemic malformations such as micrognathia and congenital heart disease. In addition, patients with Emanuel syndrome may have seizure disorders. We experienced anesthetic management of a patient with Emanuel syndrome who underwent palatoplasty. This patient had received tracheotomy due to micrognathia. In addition, he had atrial septal defect, mild pulmonary artery stenosis, and cleft palate. Palatoplasty was performed without any complication during anesthesia. Close attention was directed to cardiac function, seizure, and airway management.