In this work, the concept development, system layout, component simulation and the overall DOE system optimization of a HT-PEM fuel cell APU with a net electric power output of 4.5kW and an onboard methane fuel processor are presented. A highly integrated system layout has been developed that enables fast startup within 7.5min, a closed system water balance and high fuel processor efficiencies of up to 85% due to the recuperation of the anode offgas burner heat. The integration of the system battery into the load management enhances the transient electric performance and the maximum electric power output of the APU system. Simulation models of the carbon monoxide influence on HT-PEM cell voltage, the concentration and temperature profiles within the autothermal reformer (ATR) and the CO conversion rates within the watergas shift stages (WGSs) have been developed. They enable the optimization of the CO concentration in the anode gas of the fuel cell in order to achieve maximum system efficiencies and an optimized dimensioning of the ATR and WGS reactors. Furthermore a DOE optimization of the global system parameters cathode stoichiometry, anode stoichiometry, air/fuel ratio and steam/carbon ratio of the fuel processing system has been performed in order to achieve maximum system efficiencies for all system operating points under given boundary conditions.