This paper proposes a model of proton exchange membrane (PEM) fuel cells for real-time applications, with a 2-dimensional model of mass flow in the channel layer and a 1-dimensional model of electrochemical and mass diffusion in the diffusion layer and polymer membrane. It is also shown how an optimized program based on finite difference and finite volume methods may be developed for embedded applications, and how the error, convergence and hardware properties of this program may be analyzed to determine whether such a program can be uploaded to a real-time controller. New ideas for increasing the real-time simulation speed are given and discussed. An experimental validation of the model is done. Results from the 2-dimensional real-time mass flow model are presented and discussed, as well as performance results of the real-time simulation model. (C) 2014 Elsevier Ltd. All rights reserved.