Acetic acid (HAc), one of the major inhibitory compounds present in all lignocellulosic biomass hydrolysate, can reduce the rate and yield of bioethanol production. Electrodialysis (ED) is an electrochemical non-solvent based separation process that can selectively separate ionic species from aqueous solutions through the use of ion selective membranes and electric field potential. Two ED cell configurations at three constant applied potentials (5, 10, and 15 V) were tested for removal and recovery of HAc from a model solution of corn stover hydrolysate. The uses of bipolar membrane (configuration 1) and cation-exchange membrane (configuration 2) in an ED stack demonstrated significantly different effects on system performance in terms of: demineralization rate, acetic acid removal rate, current efficiency, and energy consumption. The demineralization and mineralization of feed and recovery solutions, respectively, increased with increasing applied voltage for both configurations. Configuration 1 showed 1.5–2 times higher initial electrical resistance at lower applied voltages compared to configuration 2. The HAc flux and removal rate increased with increasing electric potential, and were significantly higher in configurations 2 than 1. The present work indicates that a cation exchange membrane operating at 10 V is optimal for recovering HAc from a model corn stover hydrolysate solution.