We developed a dental fiberscope with a navigation system. The aim of this study is to direct the position of the tip of the endoscope fiber in the root canal via our navigation system. The distinguishing characteristic of our system is that it could be particularly practical in narrow spaces, such as those involving endodontic treatment typical of root canals. We were subsequently able to precisely indicate the relation of the position between the device and the teeth on the 3D model on the monitor. We inspected our navigation system using both the phantom model and the reconstructed 3D model. From this we could comprehend the relation of the position between the teeth and the device, and aim precisely at the lesion. If we are able to realize the correct position of the endoscope, we can safely and accurately deliver laser irradiation to the lesion. Consequently, the application of the endoscopic navigation system could increase the success rate for root canal treatments with recalcitrant lesions.