Equatorial Electrojet is a narrow current stream flowing to the east during daytime hours in the low-latitude ionospheric E region. This current acts as a channel and can cause distortions in the signals used for passive radar systems. In this study, a channel model for the equatorial electrojet is created and the changes that occur when FM signals pass through this channel are investigated. For this, equatorial electrojet is first modeled as a multilayer channel using Gaussian random processes according to physical properties. A VHF FM radio signal whose characteristics have been specified was then reexamined after it was passed through this channel. Thus, the effects of the equatorial electrojet flow on the ambiguity function performance of the FM radio signals have been revealed.