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A second-order sliding mode strategy to control the breathing subsystem of a polymer electrolyte membrane fuel cell stack for transportation applications is presented. The controller is developed from a design model of the plant derived from open literature, and well suited for the design of second-order sliding mode strategies. Stability issues are solved using a super twisting algorithm. The resulting approach exhibits good dynamic characteristics, being robust to uncertainties and disturbances. Simulations results are provided, showing the feasibility of the approach.