PC index characterizes magnetic activity generated in polar caps by R1 FAC system related to the solar wind electric field EKL. The PC index is calculated separately by data on magnetic disturbance values δF at stations Thule (PCN) and Vostok (PCS) with use of the “unified PC derivation method” taking into account statistically justified relationships between values of EKL and δF at these stations. Nevertheless, discrepancy between PCN and PCS indices is regularly observed: the value of difference ΔPC = PCN-PCS demonstrates the obvious seasonal variation and strongly increases in periods of high magnetic activity, the ΔPC values being the highest (>1 mV/m) in epochs of solar activity maximum and being the lowest (<0.5 mV/m) in the quiet periods. Analysis of discrepancies ΔPC, carried out by data on the 1-min definitive PCN and PCS indices for 22 year (1997–2022), showed that difference between the daily PCN and PCS values is caused by influence of the azimuthal BY IMF component, which generates the specific BY FAC system with reverse polarity of field-aligned currents in the northern and southern hemispheres. Effect of these currents, which is opposite in northern and southern polar caps, critically distorts the regular ionospheric current systems related to EKL field influence, resulting in discrepancy of corresponding PCN and PCS indices.