Microbial fuel cell (MFC) is attractive for research community as a promising bioelectricity production technology using organic waste. However, due to low performance and erroneous reproducibility and replicability, MFC lacks industrial application. Additionally, the nonlinear dynamic behavior of MFC, along with the involvement of electrochemistry and biology in mathematical models, makes it difficult to comprehend and simulate. To overcome these barriers, this study provides a simulation platform for conducting theoretical studies using a fundamental mathematical model of MFC. This novel Simulink/MATLAB model is based on mass balance across both compartments of MFC, and provides power density as a function of a wide range of performance-affecting parameters. Model validation depicts only 2%–10% error. This model can provide a stepping stone to perform theoretical optimization and industrial application studies in future. By varying the values of different parameters; studies may be performed to spot optimum values of the most sensitive parameters. Therefore, using the proposed tool paves the path for further improvements in design, cost effectiveness and performance efficiency that ultimately promises up-scaling of MFCs as a renewable and alternative energy resource.