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A reactive transport mathematical model was developed to simulate the electrochemical oxidation of perfluorooctanoic acid and perfluorooctanesulfonic acid in porous electrodes. The performance and sensitivity of the electrode were evaluated by varying five input parameters (specific surface area, electrode thickness, electrode conductivity, pore velocity, and applied potential). Sensitivity analysis was carried out via Latin hypercube sampling, Spearman’s rank-order correlation coefficients, and Sobol’s analysis for five performance metrics (outlet concentration, energy per log removal of the contaminant, pumping energy, removal rate, and fractional utilization of the electrode). High sensitivity to input parameters related to the electrode thickness and surface area was observed. Higher fluxes improve mass transfer in the electrode, but lower fluxes lead to better conversion and lower energy consumption due to longer residence times. Analysis of reactors in a series model suggests that increasing the length or the specific surface area of porous electrodes and operating under conditions that minimize the number of reactors may be the most energy-efficient and cost-effective approach. This modeling approach can be used to understand how operating parameters, material properties, and energy consumption of porous electrodes can inform design decisions.