Alternative fuels and innovative powering systems are recognized as essential for clean and sustainable aviation practices, performance improvements and emission reductions. This paper proposes a new hybrid turbofan and molten carbonate fuel cell (MCFC) system consisting of a steam reformer, a water gas shift reactor, and a catalytic burner. Five potential fuels are employed, including ethanol, methane, hydrogen, dimethyl ether, and methanol with different mass fractions to constitute five fuel blends. Thermodynamic analyses are conducted to study the proposed hybrid MCFC-turbofan performance, and the results are compared with a kerosene-based turbofan. It is found that a traditional turbofan performance can produce 42 MW with 59% energetic efficiency and 71% exergetic efficiency, whereas the hybrid MCFC turbofan can produce 40 MW by mixing all the five alternative fuels, but with higher performance of 65% and 80% energetic and exergetic efficiencies, respectively. Also, the CO2 emissions are substantially reduced by 75%. The fuel blends provide better performance and much lower CO2 emissions.