In recent years, the aircraft industry is heading towards the concept of the More Electric Airplane (MEA). Previous research has investigated the possibility of integrating Dual Chamber Solid Oxide Fuel Cells (DC-SOFC) with the auxiliary power unit (APU) of the aircraft. This paper evaluates the merits of integrating the recently proposed Flame-assisted Fuel Cells (FFCs) with the APU gas turbine system. The syngas composition for fuel-rich combustion is studied using chemical equilibrium analysis of Jet-A/air at 8 Bar and 1073 K. The results show the potential for reforming Jet-A fuel to 22% Carbon Monoxide and 18% Hydrogen in the exhaust at an equivalence ratio of 2.4. The paper also reports how the efficiency of power generation changes when FFCs are placed in the combustor of a turbine in the APU. The maximum theoretical electrical efficiency of the FFC/combustor and the area and weight of the fuel cell required to generate the design power is calculated. The FFC offers a viable substitute for the DC-SOFC to be integrated with the APU.