To deal with the intermittency of renewable energy resources, hydrogen as an energy carrier is a good solution. The Polymer Electrolyte Membrane Fuel Cell (PEMFC) as a device that can directly convert hydrogen energy to electricity is an important part of this solution. However, durability and cost are two hurdles that must be overcome to enable the mass deployment of the technology. In this paper, a management system is proposed for the fuel cells that can cope with the durability issue by a suitable distribution of electrical power between cell groups. The proposed power electronics architecture is studied in this paper. A dynamical average model is developed for the proposed system. The validation of the model is verified by simulation and experimental results. Then, this model is used to prove the stability and robustness of the control method. Finally, the energy management system is assessed experimentally in three different conditions. The experimental results validate the effectiveness of the proposed topology for developing a management system with which the instability of cells can be confronted. The experimental results verify that the system can supply the load profile even during the degradation mode of one stack and while trying to cure it.