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Microbial fuel cells use bacteria to generate electrical energy and are used for lower power density applications. This paper studies the effect of operational parameters on the performance of a microbial fuel cell. The effect of length of the anode compartment, inlet acetate concentration, acetate flow rate, temperature, thickness of the membrane and bio-film conductivity on the performance of the fuel cell is modeled. The thickness of the membrane is found to play a very limiting role in affecting the performance of the fuel cell. However, the length of the anode compartment, acetate flow rate and bio-film conductivity are found to play a significant role in the performance of the fuel cell. Model results are compared with experimental data and found to compare well.