This paper presents the design of a sliding mode control strategy through an input decoupling of an hybrid fuel cell based system. The hybrid system is composed by a fuel cell stack and a Supercapacitors module, connected to a single DC bus. A continuous conduction mode MIMO model is considered and the control strategy for the system is discussed. The latter is developed using a diffeomorphism to decouple the control inputs to surface interactions. Finally, an adaptive switching function for the two inputs is designed to robustly reject system perturbations and parameters variations. The control strategy is then evaluated through extensive simulation, considering strong load demand variations.