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This paper presents a novel design for a portable fuel cell system. Since the merits of supercapacitors in fuel cell systems have been explored before, this design adds functionality and uses supercapacitors as an energy storage medium that can store energy and initiate fuel cell operation. This method eliminates the need for batteries and additional circuitry normally required to initiate fuel circulation in portable fuel cell systems. Furthermore, this design uses three different control modes, which are digitally implemented and are automatically selected based on the state of the system. This allows for autonomous operation of supercapacitor charging and normal fuel cell operation. A 20 W prototype direct borohydride fuel cell converter was designed and tested. A design procedure for choosing the supercapacitor is outlined. The advantages and limitations of the novel sequence and hardware architecture are presented.