A scheme is provided for reducing the degree to which EMI from high voltage components of a fuel cell system or a fuel cell powered vehicle is induced in low voltage components of the system or vehicle. In accordance with one embodiment of the present invention, the electrical components of the system's high voltage region and the electrical components of the system's low voltage region are positioned such that, absent EMI shielding structure between the high and low voltage components, a substantial amount of EMI from the high voltage components would be induced in the low voltage components. EMI shielding structure is configured to define a conductive enclosure about the high voltage region and the low voltage region and a conductive EMI barrier between the high voltage region and the low voltage region.