Sustainable aviation attracts the attention of academic and industrial research with the aim of lowering the environmental impact and reducing greenhouse gas emissions. This paper presents two proposed high bypass three-shaft turbofan engines combined a molten carbonate fuel cell (MCFC- turbofan) and a solid oxide fuel cell (SOFC-Turbofan). Energy and exergy analyses are conducted to investigate the performance of the aircraft at the cruising operation mode. The used fuels are kero- sene and an alternative fuel blend of 75% methane and 25% hydrogen. The results show that the base turbofan has a maximum thrust force of 153 kN, while the SOFC- and MCFC-turbofans have 116 kN and 107 kN, respectively. The thermal and exergy efficiencies are 43.4% and 52% for the base-turbofan, 52.8% and 66.2% for the SOFC-turbofan, and 71% and 87.6% for the MCFC-turbofan. The carbon emissions are reduced from 18 kg/s to about 3.7 kg/s using the alternative fuel blends. The turbofan engine weight increases by 18% using the SOFC and 40% using the MCFC, while the thrust-to-weight- ratio is reduced from 2.7 for the base-turbofan, to 1.5 for the SOFC-turbofan, and 1.06 for the MCFC- turbofan. Adding a fuel cell increases the engine weight but also improves the system performance and reduces the emissions.