Acid-alkaline electrolyzers utilize an acidic catholyte and alkaline anolyte, which lower the thermodynamic voltage requirement for water splitting. Experiments have demonstrated the feasibility of acid-alkaline electrolyzers with proton exchange membranes, but a mathematical model has yet to be developed to understand their operation. This work developed a multiphysics model of a batch acid-alkaline electrolyzer with a H2SO4 catholyte, a NaOH anolyte, and a proton exchange membrane. The model was formulated in COMSOL Multiphysics® and validated using experimental current vs. voltage data in literature. The electrolyzer’s reactions and ion transport were analyzed based on the electrolyte potential, concentration profiles, and ion fluxes calculated by the model. The charge imbalance due to the consumption of H+ and OH- in the catholyte and anolyte, respectively, is addressed by Na+ transport from the anolyte to the catholyte. This contradicts the prevailing hypothesis that electroneutrality in a proton exchange membrane acid-alkaline electrolyzers is preserved by the Second Wien Effect, or water splitting in high electric fields. H+ is transported from the catholyte to the anolyte, which results in undesired acid-base neutralization. This is minimized by increasing the applied voltage, which shows a tradeoff between power and reactant consumption. Na+-selective membranes also hinder the neutralization reaction, but their realization is challenging due to the smaller Stokes radius of H+. The proposed model can be used to optimize the parameters of a batch electrolyzer and aid in the design of a continuous electrolyzer stack.