A thermal energy model for the direct methanol fuel cell (DMFC) is presented, based on the differential thermal energy conservation equation. The model is used to predict the thermal behaviour of a DMFC stack comprising of many large cells in a bipolar arrangement. The model allows an assessment of the effect of operating parameters (feed and oxidant inlet temperature, flow rate and pressure, operating current density), and the system design (active area, material properties and geometry) on the temperature profile along the stack and the interactions between the various components in the cell stack. The model is designed to enable the fuel cell system designer to estimate, insulation requirements, auxiliary equipment sizing and required thermal duties and response. Furthermore, the model can be used to decide on the optimum set of operating conditions for an efficient thermal management of the whole process.