We report a two-stage orthognathic operation for a 16-year-old boy with a repaired isolated cleft palate. He had a severe class III malocclusion with an overjet of 20.4 mm. In the first stage, we did an anterior subapical segmental osteotomy with symphyseal ostectomy to reposition the mandibular anterior segment posteriorly and to reduce the transverse width of the mandible. During the second stage, we did a maxillary advancement by Le Fort I osteotomy, mandibular set-back by sagittal split osteotomy, reduction genioplasty, and shortening of the tongue. This unique two-stage surgical and orthodontic treatment considerably improved his overall facial aesthetics and occlusion.