Background: Reconstruction of mandibular and maxillary defects resulting from malignant tumors has remained a complex challenge in recent years. Defects caused by tumors—as well as trauma, inflammatory diseases, and congenital anomalies—lead to impaired essential functions such as mastication, swallowing, and speech. Prior to the 1950s, reconstruction of maxillofacial hard tissue was not commonly performed. Instead, metal plates were used to reestablish bony continuity, and surrounding tissues were utilized to close soft tissue defects, without effectively restoring function. With modern advances in three-dimensional (3D) virtual planning, it is now possible to accurately plan free bone flaps for reconstructing jaw defects. During surgery, manually bending reconstruction plates to fit donor bone precisely is often not feasible. Preoperative 3D planning allows for precise fabrication of surgical guides and fixation plates, improving accuracy and significantly reducing operative time. Additionally, incorporating dental implant planning into the reconstruction process facilitates restoration of both structural and functional outcomes. Aim: To evaluate the outcomes of mandibular defect reconstruction using scapular free flaps in Mongolia and explore potential approaches to optimize the technique. Materials and Methods: This was a case study series. Data from reconstructive surgeries performed at the National Cancer Center of Mongolia, Central Dental Hospital, and the Mongolia-Japan Hospital were collected. Variables included patient age and sex, etiology of the mandibular defect, size of the scapular bone segment, operative time, ischemia time of the free flap, number of vascular anastomoses performed, and pedicle length. For 3D planning, CT scans of the patient's head and lower limb (slice thickness <1 cm) were used to generate 3D models via the 3D Slicer software. Cutting guides for the mandible and scapula (ASIGA), as well as the reconstruction models (AMS), were printed using a 3D printer. Results: A total of 400 free flap reconstructions were performed during the study period. Of these, 29 cases involved reconstruction of mandibular defects using scapular free flaps. The mean age of patients was 40.0 ± 18.3 years, with 52% (15 patients) being female. The etiologies of the defects included malignant tumors (13 cases, 45%), benign tumors (6 cases, 21%), and pre-existing defects (10 cases, 34%). In one case, tumor resection and mandibular reconstruction were performed using 3D planning. The total operative time was 9 hours and 30 minutes, and the ischemia time was 2 hours and 40 minutes. Conclusion Between 2012 and 2025, a total of 29 mandibular reconstructions using scapular free flaps were performed in Mongolia. Traditional reconstruction methods were associated with prolonged ischemia time. The use of 3D surgical planning has shown potential in significantly reducing ischemia time and improving surgical outcomes.