This article is focused on an original control approach applied to a transportation system that includes a polymer electrolyte membrane fuel cell (PEMFC) as the main energy source and supercapacitors (SC) as the energy storage backup. To interface the SC with the DC bus of the embedded network, a two-port bidirectional DC-DC converter was used. To control the system and ensure its stability, a reduced-order mathematical model of the network was developed through a nonlinear control approach employing a differential flatness algorithm, which is an attractive and efficient solution to make the system stable by overcoming the dynamic issues generally met in the power electronics networks of transportation systems. The design and tuning of the system control were not linked with the equilibrium point at which the interactions between the PEMFC main source, the SC energy storage device, and the loads are taken into consideration by the proposed control law. Besides this, high dynamics in the load power rejection were accomplished, which is the main contribution of this article. To verify the effectiveness of the developed control law, a small-scale experimental test rig was realized in the laboratory and the control laws were implemented in a dSPACE 1103 controller board. The experimental tests were performed with a 1 kW PEMFC source and a 250 F 32 V SC module as an energy storage backup. Lastly, the performances of the proposed control strategy were validated based on real experimental results measured during driving cycles, including motoring mode, ride-though, and regenerative braking mode.