The computer-aided design/computer-aided manufacturing (CAD/CAM) virtual orthodontic system produces customized brackets, indirect bonding jigs, and archwires based on a three-dimensional virtual setup. In surgical cases, this system helps to visualize the final occlusion during diagnosis and to efficiently plan individualized presurgical orthodontic treatments. A 20-year-old female patient with a skeletal Class III malocclusion, maxillary protrusion, and lip protrusion was successfully treated with orthognathic surgery and orthodontic treatment with maxillary first premolar extractions. The CAD/CAM system was applied for efficient treatment, with a total active treatment time of 16 months. In this case report, the applicability of the CAD/CAM virtual orthodontic system for orthognathic surgery cases is demonstrated. Suggestions are also made to overcome the limitations and to maximize the advantages of this system during orthodontic treatment of patients undergoing orthognathic surgery.