A new method for computing convection heat transfer coefficients in axial flux permanent magnet synchronous machines (AF-PMSMs) is introduced. The method is based on a two-step finite element analysis (FEA). In the first step, a simple 2D model is introduced and fluid flow and temperature fields are studied using computational fluid dynamic (CFD) technique. Convective heat transfer coefficients for all heat transfer surfaces of the model are extracted from CFD analysis and are then used as inputs to a 3D thermal finite element model. Two case studies are considered to check the accuracy of the abovementioned two-step method. One of the case studies is an air-cooled AF-PMSM that has air inlet and outlet on its enclosure and the other case is a totally enclosed AF-PMSM. The correctness of the mentioned method is verified by practical measurements on the second case. In addition, an experimental set-up is conducted to measure the temperature of different parts of the second case. It is observed that the results of the two-step CFD-FEA model are in good agreement with the experimental data. In the other case, the effect of inlet air velocity on heat transfer coefficients, as well as the thermal behaviour of the machine are explored.