Fouling is one of the major problems in electrodialysis. The aim of the present work was to investigate the effect of five different solution flow rates (corresponding to Reynolds numbers of 162, 242, 323, 404 and 485) combined with the use of pulsed electric field (PEF) current mode on protein fouling of bipolar membrane (BPM) during electrodialysis with bipolar membranes (EDBM) of skim milk. The application of PEF prevented the fouling formation by proteins on the cationic interface of the BPM almost completely, regardless of the flow rate or Reynolds number. Indeed, under PEF mode of current the weight of protein fouling was negligible in comparison with CC current mode (0.07 ± 0.08 mg/cm2 versus 5.56 ± 2.40 mg/cm2). When a continuous current (CC) mode was applied, Reynolds number equals or higher than 323 corresponded to a minimal value of protein fouling of BPM. This positive effect of both increasing the flow rate and using PEF is due to the facts that during pauses, the solution flow flushes the accumulated protein from the membrane while in the same time there is a decrease in concentration polarization (CP) and consequently decrease in H+ generation at the cationic interface of the BPM, minimizing fouling formation and accumulation.