Fuel cell vehicle technology has drawn wide attention because of the environmental and economic issues related to excessive usage of fossil fuels. Fuel cells are known for their unidirectional environmental friendly operation; however, they have low power density and suffer from slow dynamics. Therefore, a sole fuel cell system cannot meet the requirements of an electric vehicle whose power demand is quite dynamic. In a way of hybridizing a fuel cell with energy storage devices, it can be possible to overcome aforementioned problems. A plug-in fuel cell hybrid electric vehicle system, equipped with a battery and an ultra-capacitor, is proposed in this work. In this system, a single multi-input converter is utilized to control source energies. Moreover, this work develops a computationally efficient energy management strategy which is essentially a frequency decoupling method basically taking the advantage of easily applicable low pass filters. In this strategy, a polynomial scales the fuel cell and battery power levels to regulate ultra-capacitor voltage. The whole system is tested via a simulation model after the detailed analysis of the multi-input converter.