Fuel cells are clean power sources that have much higher energy densities and lifetimes compared to batteries. However, fuel cells have limited load following capabilities and cannot be efficiently utilized if used in isolation. In this work, we consider a hybrid system where a fuel cell based hybrid power source is used to provide power to a DVFS processor. The hybrid power source consists of a room temperature fuel cell operating as the primary power source and a Li-ion battery (that has good load following capability) operating as the secondary source. Our goal is to develop polices to extend the lifetime of the fuel cell based hybrid system. First, we develop a charge based optimization framework which minimizes the charge loss of the hybrid system (and not the energy consumption of the DVFS processor). Next, we propose a new algorithm to minimize the charge loss by judiciously scaling the load current. We compare the performance of this algorithm with one that has been optimized for energy, and demonstrate its superiority. Finally, we evaluate the performance of the hybrid system under different system configurations and show how to determine the best combination of fuel cell size and battery capacity for a given embedded application.