Electrodialysis (ED) is frequently used in the desalination of whey. However, the fouling onto the membrane surface decreases the electrodialysis efficiency. Pulsed Electrodialysis Reversal (PER), in which short pulses of reverse polarity are applied, is expected to decrease the fouling onto membrane surface during ED. Three (PER) regimes were applied in the desalination of acid whey (pH ≤ 5) to study their effects on the membrane fouling and the ED efficiency. The PER regimes were compared to the conventional ED as the control. For each regime, two consecutive runs were performed without any cleaning step in-between to intensify the fouling. After the second run, the membranes were subjected to the Scanning electron microscope (SEM) imaging and contact angle measurement to investigate the fouling on the membrane surface in different regimes. The ED parameters in the case of conventional ED were almost the same in the first and the second runs. However, the parameters related to the ED efficiency including ED capacity, ash transfer, and ED time, were deteriorated when the PER regimes were applied. The contact angle values indicated that the fouling on the diluate side of anion exchange membranes was more intensified in conventional ED compared to the PER regimes. The SEM images also showed that the fouling on the diluate side of both cation and anion exchange membranes under PER regimes was reduced in respect to the conventional ED. However, the back transfer to the diluate compartment when the reverse pulse was applied is dominant and lowers the ED efficiency slightly when the PER is applied.