In this study, we propose an unmanned aerial vehicle (UAV) navigation system using LED panels and QR codes as markers in an indoor environment. An LED panel can display various patterns; hence, we use it as a command presentation device for UAVs, and a QR code can embed various pieces of information, which is used as a sign to estimate the location of the UAV on the way of the flight path. In this paper, we present a navigation method from departure to destination positions in which an obstacle lies between them. In addition, we investigate the effectiveness of our proposed method using an actual UAV.