The line-of-sight(LOS) rate is estimated using Kalman filter in Radio-Frequency(RF) seeker. For the two axis gimbaled seeker, proper system modeling is considered and the basic filter structure is set up. The main issue for Kalman filter is choosing the proper process and measurement noise. For the measurement process, the signal to noise ratio(SNR) and other components are introduced. To cope with the eclipse problem or other abnormal seeker status, the pseudo input signal concept is proposed. By conditioning abnormal signals, the LOS rate estimation performance is increased. The process noise is also an important factor in the propagation phase. The analytical approach on a process noise component is performed and a reliable region for the filter is calculated based on the eigenvalue analysis. Some numerical simulations are performed to check the validity of suggested algorithm.