Passive radar systems operate by employing cooperative or noncooperative radio signals in the environment in order to sense remote targets. This particular feature of passive radar systems provides unique opportunities to expand the coverage map of conventional radars. In using passive radar systems, any undesirable obstacle between the transmitted signal and the path of the desirable target can cause obliteration on the source signal and destroy its key correlative properties. The equatorial electrojet (EEJ) can have unfavorable effects on the operation of the prospective passive radar systems, which can conceivably employ very high frequency frequency-modulated (FM) radio signals around the magnetic equator. The EEJ is a strong flow of current in the upper atmosphere around 100 km of altitude over the magnetic equator. Because of the density irregularities within, the ionospheric current is a geophysical obstacle for the deployment of passive radar systems near those latitudes. In this paper, we assess the effects of the EEJ on the operation of FM-based passive radar systems. First, we simulate the EEJ as a communication channel based on its physical properties by using Gaussian random processes. We simulate the propagation of FM signals through this communication channel and determine the changes in their correlative properties. Finally, we present the experimental data that were collected near the magnetic equator that demonstrates the malfunction of the FM-based passive radar systems due to the EEJ. These observations and numerical results show that careful considerations must be taken when implementing FM-based passive radar systems at equatorial latitudes.