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This paper presents the analysis and design of a hybrid fuel cell battery auxiliary power unit (APU) for remote applications implemented with virtual and rapid prototyping techniques. The fuel cell is the main energy source working in low frequency bandwidth while the battery compensates the transient peak power needs. The control of the fuel cell system using two techniques, the first-order based control where the fuel cell delivers the filtered load current and a fuzzy based control. The simulation show that the last one permits the fuel cell to working most of the time in its optimal working zone as well as maintaining the battery state-of-charge in its optimal windows whatever the initial sate-of-charge.