In this paper, a new control-oriented modeling methodology for the thermal dynamics of water-cooled Proton Exchange Membrane Fuel Cells (PEMFCs) is presented and validated. This methodology is not only useful for control applications, but also can be used for predicting the temperature variation across the stack, allowing to monitor its operation. The methodology has been validated in a real 600-W, 20-cells, water cooled PEMFC, with encouraging results for both the stationary and the transient states. Results show that the proposed methodology is accurate and suitable for control purposes.