The transoral route is a standard surgical approach to the anterior craniovertebral junction, where neuronavigation is difficult secondary to the mobility of the cervical spine in relation to the cranium. We describe the use of neuronavigation combined with intraoperative 3D C-arm to direct our approach and resection of two lesions of the craniovertebral junction. Neuronavigation was employed in planning of incision, bony resection, and assessment of lesion resection. Both patients underwent transoral approach without complication using this method. Frameless stereotaxy with BrainLab VectorVision and 3D C-arm is an effective method of neuronavigated approach to the anterior craniocervical junction, which may contribute to the safety of this approach.