Prader-Willi syndrome (PWS) is a complex disorder that affects multiple systems and may cause craniofacial and dentofacial abnormalities. However, there is still a lack of evidence in the literature regarding the progress of orthodontic treatment in patients with PWS. This case report describes the successful orthodontic treatment of a patient with PWS. A girl, 9 years 0 months of age, who had been diagnosed with PWS had protruding maxillary incisors and a convex profile. Her malocclusion was due to the posteriorly positioned mandible. Screening tests for sleep apnea syndrome showed that she had sleep-disordered breathing, including obstructive sleep apnea and bruxism. We also observed an excessive overjet of 10.0 mm, a deep overbite of 6.8 mm, and the congenital absence of the mandibular second premolars. The patient was diagnosed with an Angle Class II malocclusion and a skeletal Class II jaw-base relationship with a deep overbite. Functional appliance therapy with mandibular advancement, which can enlarge the upper airway and increase the upper airspace, was performed to prevent further deterioration of the patient's obstructive sleep apnea. An acceptable occlusion with a proper facial profile and functional excursion were achieved without interference after comprehensive 2-stage treatment that incorporated orthodontic therapy for the patient's excessive overjet and deep overbite. The resulting occlusion was stable, and the occlusal force and the contact area gradually increased over a 2-year retention period. These results suggest that orthodontic treatment offers the opportunity to greatly improve the health and quality of life of people with PWS.