The article presents a new method of restoring the electron density profile (Ne) according to data from the Irkutsk Incoherent Scatter Radar (IISR). This method has been developed taking into account the Faraday rotation of the polarization plane, which leads to fading at the output of the IISR linearly polarized antenna. The concept of the method consists in fitting a height variation of electron density by a parametric model. As the model, a combination of two Chapman layers was used. This approach made it possible to implement a fully automatic data processing mode and increase the stability of the recovery of the Ne profile, especially according to data obtained during a period of low solar activity when the signal-to-noise ratio is low. Accuracy was increased by eliminating a number of operations leading to instability of data recovery in the presence of noise. The new method enabled fully automatic processing of long data series in the period 2007–2015.