Utilization of electrochemical devices, such as batteries and fuel cells, is getting more widespread and there is an urgent need for their further improvement in terms of performance and cost efficiency. The main component of these technologies is the electrode. Topology optimization has a significant potential for designing innovative structures for porous electrochemical reactors (e.g., electrodes). Most studies that used this powerful tool only focused on the mathematical algorithm rather than providing a detailed physicochemical explanation of the optimization process. This study aims to find the optimal materials distribution layout in a porous electrochemical system and explain how such an optimal design solution is achieved from a fundamental perspective. A mathematical model is developed to characterize the system performance. In addition, using the concept of non-equilibrium thermodynamics, a model is developed for the assessment of local and global entropy generation. The comparison between the initial uniform layout and the optimized structure for the porous medium shows that the latter reduced the system total overpotential (dissipation) by 42.2%, thanks to a better balance between the transport and rate processes. From a fundamental point of view, this improvement is related to the reduction of global entropy generation, which itself happens because of more equipartitioned entropy generation in the system.