Hybridization of fuel cell with energy storage system is commonly used to obtain simultaneously high power and energy density along with fast transient response. Energy storage system is normally connected to fuel cell either directly or through power converter interfaces. This paper proposes a novel reconfigurable structure in which energy storage system can be interchangeably used both in direct or isolated modes. This proposed structure enables extraction of maximum power output during various modes of operation of hybrid system. Ultracapacitor is chosen as energy storage system in the present paper, as it has faster transience compared to batteries. A multi objective energy management algorithm is proposed which ensures higher utilization of the converters and ultracapacitor, in addition to improved fuel cell performance. The merits of the proposed reconfigurable hybrid system are illustrated through simulation and experimentation and it has been observed that the converters are effectively utilized with tight load voltage regulation. Copyright (C) 2015, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.