Ammonia and biomass-derived fuel are carbon-neutral fuels. Therefore, there are no carbon emissions after power generation. While those fuel supplied SOFC systems have an advantage without CO2 emissions, the influence on the system performance should be quantified to compare with conventional fuel supplied SOFCs. In this study, 100kW scale SOFC system model shown in Fig.1 (a) was evaluated in heat and mass balance analysis to consider the effect of supplied fuel on the SOFC system performance. A protonic ceramic electrolyte application was also evaluated to increase its electrical efficiency. The carbon-neutral fuel fed protonic ceramic fuel cells (PCFCs) had an advantage to enhance the electrical efficiencies compared with the same fuel fed typical SOFCs shown in Fig.1 (b). As highly efficient power generation system without CO2 emissions, the effects of carbon-neutral fuels on the electrical efficiency and the emission reduction were investigated by the process simulation of total fuel cell system.