Asymmetric flow field flow fractionation (AF4) is an efficient size-based separation technique for the characterization of submicron size particulates. In AF4, membranes having various molecular weight cutoff sizes are used as a barrier to retain particles while allowing the carrier fluid containing electrolytes to permeate. Here, we have hypothesized that electrolyte rejection by the barrier membrane leads to the accumulation of electrolytes in the membrane channel during operation. Electrolyte accumulation can cause various adverse effects that can lead to membrane fouling. An instrument setup containing a conductivity detector was flow out assembled, and the rejection of commonly used carrier (to waste) electrolytes such as trisodium citrate, ethylenediaminetetraacetic acid, sodium chloride, and ammonium carbonate was evaluated by varying the concentration, cross-flow rate, focusing flow rate, membrane material type, and cutoff sizes. The results showed that electrolyte rejection increased with a decrease in the electrolyte concentration and the molecular weight cutoff size (pore size) or with an increase in the charge state of the anion in the carrier electrolytes. We proposed an electrostatic repulsion-based rejection mechanism and verified it with the measurement of the rejection rate while varying the electrolyte concentration in the running media.