Tracking micro-sized insects is one of the challenges of protecting ecosystems and biodiversity. In this study, we propose an approach for the autonomous tracking of micro-sized flying insects, and develop an unmanned aerial vehicle (UAV)-based robotic system. The Kalman filter is applied to the received signal strength emitted from radio telemetry to estimate the position while reducing the measurement error and noise. The autonomous tracking strategy is a method in which the UAV rotates at one point to measure the signal strength and control its position in the strongest direction of the signal. We also design a system architecture comprising a tracking sensor system and a UAV system for micro-sized insects. The estimation and autonomous tracking of the target position by the proposed system are verified and evaluated through dynamic simulation. Therefore, in this study, we propose and validate a UAV-based tracking system for micro-sized flying insects, which has not been proposed in studies conducted thus far.