In our previous studies, we reported that the flux change during nanofiltration (NF) of whey could be predicted by our theoretical analysis method. In this method, it is hypothesized that whey comprises both permeable and non-permeable solutes. Permeable solute can pass through an NF membrane but non-permeable solute cannot. We also found that the exchange of citric and phosphoric acids, amongst others, classified as non-permeable solutes, with chloride ions, classified as a permeable solute, by passage through an anion-exchange column in chloride form could increase the desalination ratio during NF of whey. In this study, we investigated whether our analysis method could be used to predict the flux change of anion-exchanged whey (IE whey). The ratio of non-permeable solute to total solute quantities in IE whey differed from that in the original whey, reflecting the difference in composition. The simulated fluxes matched measured values, indicating that our analysis method is useful for predicting flux change during NF of IE whey.