Since Fuel Cells (FCs) are very expensive, its output power should be minimized when FCs are applied to hybrid powered railway vehicles with Electric Double Layer Capacitors (EDLCs). Therefore, it is necessary to clarify a reasonable method to determine the required FCs output power. In this paper, the basic view for determining the required FCs output power and EDLCs capacitance, and controlling the EDLC energy appropriately is revealed. The proposed methods are verified by numerical simulations, assuming a train operation in a typical rural line. The results of this study would contribute to the development of environment-friendly transportation system.