Fuel cells are promising devices to transform chemical energy into electricity; their behavior is described by principles of electrochemistry and thermodynamics, which are often difficult to model mathematically. One alternative to overcome this issue is the use of modeling methods based on artificial intelligence techniques. In this paper is proposed a hybrid scheme to model and control fuel cell systems using neural networks. Several feature selection algorithms were tested for dimensionality reduction, aiming to eliminate non-significant variables with respect to the control objective. Principal component analysis (PCA) obtained better results than other algorithms. Based on these variables, an inverse neural network model was developed to emulate and control the fuel cell output voltage under transient conditions. The results showed that fuel cell performance does not only depend on the supply of the reactants. A single neuro-proportional−integral−derivative (neuro-PID) controller is not able to stabilize the output voltage without the support of an inverse model control that includes the impact of the other variables on the fuel cell performance. This practical data-driven approach is reliably able to reduce the cost of the control system by the elimination of non-significant measures.