The present research work deals with prediction of hydrogen consumption of a fuel cell in an energy storage system. Due to the fact that these kind of systems have a very nonlinear behaviour, the use of traditional techniques based on parametric models and other more sophisticated techniques such as soft computing methods, seems not to be accurate enough to generate good models of the system under study. Due to that, a hybrid intelligent system, based on clustering and regression techniques, has been developed and implemented to predict the necessary variation of the hydrogen flow consumption to satisfy the variation of demanded power to the fuel cell. In this research, a hybrid intelligent model was created and validated over a dataset from a fuel cell energy storage system. Obtained results validate the proposal, achieving better performance than other well-known classical regression methods, allowing us to predict the hydrogen consumption with a Mean Absolute Error (MAE) of 3.73 with the validation dataset.