Virtual planning in craniofacial surgery has become essential for improving surgical outcomes, especially in complex cases such as patients with Apert syndrome. Technologies such as cone-beam computed tomography and intraoral scanning with three-dimensional software simulate osteotomies and maxillary/mandibular repositioning in greater detail, allowing for more precise and predictable planning. Although the use of virtual surgical planning (VSP) in orthognathic surgery has become commonplace, its use in procedures on patients with Apert syndrome before their growth completes remains under debate. From an engineering perspective, issues such as outcome prediction for soft tissues and consideration of dynamic procedures like distraction are complex. Here, we provide an overview of VSP for procedures performed in patients with Apert syndrome before the end of growth, followed by a detailed description of the planning workflow for orthognathic procedures in Apert syndrome.