In this paper a hierarchical multiscale model for microfluidic fuel cells with porous electrodes is developed for the first time. An example of the hierarchical multiscale model for all-vanadium microfluidic fuel cells is presented in this study, in which the diffusion coefficient is used as a bridge between the microscale, mesoscale, and macroscale models. Three-level theories are used to describe the microfluidic fuel cells systems. The development of the model in different time and length scales is emphasized. Results from each scale model are compared with the corresponding experimental and other reasonable data in the literature. We demonstrate that the multiscale model is able to predict the characteristics of microfluidic fuel cells more accurately than before. The hierarchical multiscale model can be a potential tool for developing, designing, and optimizing microfluidic fuel cells.