The paper presents a model-based approach to supporting battery selection for a fuel cell (FC)-based auxiliary power unit (APU). It is introduced to a case study of electrical power production and consumption management in a truck anti-idling application of a diesel-powered FC-based APU, a system under development in FCGEN, a FCH JU European project of the FP7 program. With fuel cell and related technologies increasingly competing with others in the market, they need to form complete systems with matching and well-balanced components to enable using the technology to its best. Within the whole system, the battery, serving as an energy buffer, represents a medium-cost element, but it affects the operating parameters importantly. Within the scope of this study, a purpose-oriented model of the diesel powered FC-based system is developed together with a realistic load scenario for the comparison of three batteries. The battery size and type are investigated and discussed in the light of the simulation results.