Based on mathematical modeling and numerical simulations, applicativity of various biofuels on high temperature fuel cell performance are presented. Governing equations of high temperature fuel cell modeling are given. Adequate simulators of both solid oxide fuel cell (SOFC) and molten carbonate fuel cell (MCFC) have been done and described. Performance of these fuel cells with different biofuels is shown. Some characteristics are given and described. Advantages and disadvantages of various biofuels from the system performance point of view are pointed out. An analysis of various biofuels as potential fuels for SOFC and MCFC is presented. The results are compared with both methane and hydrogen as the reference fuels. The biofuels are characterized by both lower efficiency and lower fuel utilization factors compared with methane. The presented results are based on a 0D mathematical model in the design point calculation. The governing equations of the model are also presented. Technical and financial analysis of high temperature fuel cells (SOFC and MCFC) are shown. High temperature fuel cells can be fed by biofuels like: biogas, bioethanol, and biomethanol. Operational costs and possible incomes of those installation types were estimated and analyzed. A comparison against classic power generation units is shown. A basic indicator net present value (NPV) for projects was estimated and commented.