In this paper a data-validated power-efficiency model of a diesel-powered fuel-cell-based auxiliary power unit (APU) system is used to investigate the various sizes of the power unit and the battery and to evaluate the optimal choices for specified load profiles. The challenge comes from the FCGEN (Fuel Cell-based power GENeration) EU FP7 project, where such an APU was developed. The system consists of a fuel processor, a PEM stack, and a battery providing power for the startup, shutdown, and for covering load transients; however, the developed prototype system is not optimised. Before redesigning it for mass production, the optimal size of the main components needs to be identified to enable the best possible exploitation of the technology. In this work a case-specific load profile was used and a mesh grid of scenario simulations has been performed using various sizes of the fuel cell with fuel processor as a power unit and the batteries of various capacities as an energy storage unit. For this purpose a scalable APU model, including the BoP component consumption, has been developed. Upon the analysis results, the relation for optimal combinations in terms of efficiency and degradation is proposed and the confronted tradeoffs are discussed.