We developed a dental fiberscope that can be navigated. As a result we are able to better grasp the device position relative to the teeth, aiming at the lesion more precisely. However, the device position and the precise target setting were difficult to consistently ascertain. The aim of this study is to navigate the position of tip of the dental fiberscope fiber in the root canal with our navigation system. A 3D tooth model was made from the raw dental CT data. In addition, the optical position of the measurement device, OPTOTRAK system was used for registration of the 3D model and actual teeth position and to chase the scope movement. We developed exclusive software to unify information. We were subsequently able to precisely indicate the relation of the position between the device and the teeth on the 3D model in the monitor. This allowed us to aim at the lesion more precisely, as the revised endoscopic image matched the 3D model. The application of this endoscopic navigation system could increase the success rate for root canal treatments with recalcitrant lesion.