Due to the rising problem of global warming, high-temperature fuel cells are considered to be the future of power generation. Despite its active development in recent decades, Molten carbonate fuel cells have not reached full commercialization. Degradation of the materials, cost, and performance are the factors that require optimization. The optimization of the fuel cell can be realized in many ways (e.g., materials, flow distribution, operating conditions, etc.). However, the microstructure of the fuel cell material can be one of the essential areas for optimization. Developing fuel cells require conducting a lot of experimental investigations. Often such investigations are costly and time-consuming. Because of that, various mathematical and numerical models are used. The literature overview shows a few models that account for microstructure influence on the electrochemical performance of the fuel cells. This work presents a development of the mathematical model that accounts for material microstructure (e.g., porosity, tortuosity, constrictivity) and validation thereof. The validation was based on two experiments with different microstructure parameters. This mathematical model predicts the molten carbonate fuel cell performance using anodes with different porosity. The obtained results were analyzed and discussed. Possible areas of applications and further optimization are provided.