Conventional intraoral removal of deeply impacted or ectopic mandibular third molar is challenging for limited surgical access. Because there are potential risks of inferior alveolar nerve (IAN) injury or iatrogenic mandibular fracture, several methods for the removal have been proposed. As minimally invasive and safe surgery, we report image-guided removal of deeply impacted mandibular third molar using navigation system. A 32-year-old male was referred to our department with right mandibular pain and swelling. Panoramic radiograph showed right mandibular third molar was deeply impacted and interrupted the white line of the mandibular canal. Computed tomography (CT) showed deep impacted right mandibular third molar with root projection from the lingual cortical bone, and there was resorption of lingual cortical bone and passing of mandibular nerve between roots. For mandibular navigation surgery, a resin occlusal splint with titanium markers and handle was manufactured to fix reference frame to the mandible. CT was performed preoperatively after the occlusal splint was fixed with patient's mandibular teeth, and the patient underwent image-guided removal of mandibular third molar with navigation system under general anesthesia. After reference frame was attached to the handle of the occlusal splint fixed with patient's mandibular teeth, point-based registration was performed. The crown was removed after the sectioning, and the root sectioning with calibrated bur was performed carefully to avoid injury of the IAN under navigational guidance. The roots were completely removed, and the IAN was exposed in the lingual cortical bone defect. Postoperative course was uneventful without paresthesia of the IAN.