An extended Kalman filter (EKF) to estimate the ionospheric total electron content (TEC) along the radar line-of-sight has been developed. By varying the carrier frequency of consecutive radar pulses, it is shown that the TEC along the line-of-sight becomes observable and can be estimated in real-time to a high degree of accuracy. It is shown that the filtering formulation presented here optimally reduces the randomly varying range bias caused by the irregular electron density structure in the upper atmosphere. The performance of the tracking filter is examined with a Monte Carlo simulation analysis. It is shown that for a radar located in Thule, Greenland and operating at a nominal frequency of 435 MHz (UHF), an improvement of approximately 50% in the range estimation accuracy is achieved with a frequency separation of 18 MHz between two consecutive pulses. If the frequency separation is increased to 60 MHz, the increase in accuracy is 75%. It is also shown that in the absence of frequency separation, the performance of the tracking filter presented here reduces to that of a conventional six-state EKF that does not account for the ionospheric bias.