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Aqueous electrochemical flow capacitors (EFCs) have demonstrated high-power capabilities and safety at low cost, making them promising energy storage devices for grid applications. A primary performance metric of an EFC is the steady-state electrical current density it can accept or deliver. Performance prediction, design improvements, and up-scaling are areas in which modeling can be useful. In this paper, a novel stochastic superparticle (SP) modeling approach was developed and applied to study the charging of carbon electrodes in the EFC system, using computational superparticles representing real carbon particles. The model estimated the exact values of significant operating parameters of an EFC, such as the number of particles in the flow channel and the number of electrolytic ions per carbon particle. Optimized model parameters were applied to three geometrical designs of an EFC to estimate their performance. The modeling approach allowed study of the charge per carbon particle to form the electric double-layer structure. The linear relationship between the concentration of SPs and the ionic charge was observed when optimized at a constant voltage of 0.75 V. The simulation results are in excellent agreement with experimental data, providing a deep insight into the performance of an EFC and identifying limiting parameters for both engineers and material scientists to consider.