This paper presents a tracking filter of radar beacon system (RBS) for automatic takeoff and landing of an unmanned aerial vehicle. The proposed tracking filter is designed as the decoupled tracking filter to reduce the computational burden. Also, an adaptive estimation method of the measurement error covariance is proposed to provide an improved tracking performance compared to the conventional decoupled tracking filter whenever the accuracy of RBS observations is degraded. 100 times Monte Carlo runs performed to analyze the performance of the proposed tracking filter in case of normal operation and degraded operations, respectively. The simulation results show that the proposed tracking filter provides the improved tracking accuracy in comparison with the conventional decoupled tracking filter.