Background and Objectives: Transverse maxillary deficiency is an important maxillary anomaly that is very common in society and remains current in orthodontics. The maxillary expansion has been used in treatment for a long time. While maxillary expansion can be performed with rapid maxillary expansion in young adults, it is performed with surgically assisted rapid maxillary expansion (SARME) in individuals who have reached skeletal maturity. No consensus has been reached on the most successful surgical technique or the ideal appliance for treating transverse maxillary deficiency. Accordingly, we aimed to evaluate various surgical techniques and orthodontic appliances for treating transverse maxillary deficiency using the finite element method (FEM) to identify the treatment protocol that minimizes stress on the maxillary bone and teeth. Materials and Methods: On the virtual models obtained from the cone beam computed tomography of a patient, two different incisions (the pterygomaxillary junction is separated and not separated) were made and combined using three different orthodontic appliances (tooth, bone, and hybrid assisted). Then, stresses over the maxillary bone and maxillary teeth were calculated by FEM. Results: Our results showed that when the pterygomaxillary plates were separated, fewer stresses were observed on the bone and teeth. Although hybrid-supported appliances created less stress on the teeth than tooth-supported appliances and no difference was found between bone-supported appliances, it was found that hybrid-supported appliances created less stress on the bone than the other appliances. Conclusions: The separation of the pterygomaxillary junction in the SARME operation and the use of a bone-supported or hybrid-supported appliance would place less stress on the bone and teeth.