This paper presents a coupled model of heat transfer and plastic deformation in friction stir welding (FSW), accounting for the temperature profile in the substrate near the pin. The approach is analogous to the boundary layer analysis in fluid mechanics and is based on the methodology of scaling and calibration based on published data. A model focusing on common conditions in FSW, such as relatively slow translation and high rotation velocities, a thin shear layer and the influence of the shoulder on the maximum temperature was reformulated. This paper extends previous work by considering the heat flow into the pin and an improved criterion for determining the temperature at the edge of the shear layer. The results are a set of updated closed-form expressions for the maximum temperature, the thickness of the shear layer, the shear stress around the pin, torque and thermal effect of the shoulder, applicable to all metals. The predictions from this model are verified against a comprehensive database of published experiments. Applications of this model also include the accelerated determination of procedure variables and the generalization of maps of process limits.