Compared to the other energy conversion systems, Fuel Cells are preferred in many applications due to quitter working and their sensitivity to the environment. However an energy storage system with sufficient power capacity should be incorporated with FCs to compensate its slow dynamics. Ultra-capacitors with their high power densities and fast response times are potential candidates for a solution in this aspect. In conventional methods DC bus voltage is regulated by DC/DC converters to be able to generate a voltage controlled sine waveform by controlling inverters modulation index. In this study, on the contrary to conventional methods DC bus voltage is chosen like a rectified sinusoidal waveform. By this way as the DC bus is sinusoidal the inverter is controlled as a polarity changing inverter which provides to switch inverter switches at 50 Hz. However this method requires an excessive care on DC/DC converter controls as excessive humidification and membrane drying may occur on a FCs in case of sudden changes in load demand. A group of simulation studies are done in this study to design and test the required controller and compare the method for this mentioned necessity in literature. (C) 2017 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.