Here, we describe a case of autotransplantation of a mandibular horizontally impacted third molar using a 3-dimensional (3D) model based on limited cone-beam computed tomography (CBCT) images for diagnosis, 3D morphological evaluation, preoperative treatment planning, and surgical simulation. A 27-year-old woman visited this hospital for conservative treatment of the mandibular left second molar. Intraoral radiography and CBCT images revealed a C-shaped root canal in the mesial root, and compressive resorption of the distal root due to impingement of the crown of the horizontally impacted lower left third molar. Extraction was therefore planned. Multiple tooth-jaw bone 3D models for preoperative diagnosis were fabricated using a low-cost desktop 3D printer and surgical simulation of autotransplantation performed. The autotransplantation was then performed accordingly. Cone-beam computed tomography images and 3D models were extremely useful in obtaining a stereoscopic understanding of the morphology of the transplanted tooth and its surrounding anatomical structures. At the one-year postoperative recall, the patient was able chew with the transplanted tooth without pain, and no significant abnormalities were detected on intraoral radiographs, indicating a successful postoperative clinical course. Our experience of using 3D models fabricated based on CBCT images using a desktop 3D printer for preoperative diagnosis and surgical simulation suggests that this technique is useful in tooth autotransplantation.