Solid oxide fuel cells competence in combination with gas turbine cycle has caused the obtained synthetic system to become as a new power production system in consideration of different researchers. One of the important applications of this type of hybrid systems is to use them in UAV propulsion systems and in airliners as an APU. The main purpose of this research is design of a hybrid APU equipped to solid oxide fuel cell that would be one of the basic requirements for electric power generation in larger aircrafts in the future. Design parameters and decision-making variables in analysis of this system are the compressor pressure ratio, gas temperatures entrance to turbine and the number of selected cells. The results show that the system’s increasing pressure causes decrease in the temperature of outlet gases from the turbine and the cell’s operating temperature; and this problem severely affects the productivity and efficiency of the electrical system. At 1000 ° C for entrance gases to the turbine, electrical efficiency of system is about 49 percent. Also, the maximum electrical efficiency of the system in fuel cell is estimated to be about 55 percent. The obtained result shows that in case of controlling the generated heat in the cell and effective usage of it, the overall system efficiency will be augmentable about 84 percent. On the other hand, increasing the number of cells will cause increasing electrical efficiency and reducing the overall efficiency of the fuel cell hybrid system.