A heat transfer numerical model is developed for friction stir welding of dissimilar materials Al 6061 and AZ31 alloy. Thermo-physical properties were experimentally determined for the stir zone and compared with the base alloys. Experimentally determined thermo-physical properties of the stir zone are not strictly the average values of the base alloys but exhibit a complex relationship with the microstructural features and the intermixing of Al and Mg in the weld region. The numerical model is employed to predict the temperature distribution on the advancing and retreating side. A good agreement between computed and experimentally measured results was obtained at 24-mm, 20-mm, and 16-mm tool shoulder diameter. The proposed model can be used to predict the thermal cycle, peak temperature, and thermo-mechanically affected zone for welding of dissimilar materials on friction stir welding.