Orthodontic management in patients with Apert syndrome must take into account the specific functional challenges associated with this condition—including obstructive sleep apnea syndrome, transverse and sagittal maxillary growth deficiencies, and the frequent presence of cognitive impairment. It is also essential to consider the risk of iatrogenic molar damage following frontofacial monobloc advancement or Le Fort III osteotomy, as well as the constraints related to the use of orthodontic appliances that may interfere with magnetic resonance imaging (MRI). In clinical practice, orthodontic treatment typically begins around the age of six, with an initial assessment of the indications for transverse maxillary expansion. Le Fort III osteotomy generally does not require orthodontic preparation, except for the fabrication of palatal plates in order to prevent excessive correction of the narrow palatal width during subcranial bipartition, and to control the inclination of the incisor roots to avoid injury during the intermaxillary osteotomy. Aside from these considerations, orthodontic treatment should usually be postponed until ages 14–15, except in cases where traction of impacted teeth is necessary to avoid overly prolonged therapy. Ultimately, all patients will require orthognathic surgery, preceded by comprehensive presurgical orthodontic alignment of the dental arches.