A computational fluid dynamics (CFD) model is presented for simulating the material flow and heat transfer in the friction stir welding (FSW) of 6061-T6 aluminum alloy (AA6061). The goal is to utilize the 3-D, numerical model to analyze the viscous and inertia loads applied to the FSW tool by varying the welding parameters. To extend the FSW process modeling, in this study, the temperature-dependant material properties as well as the stick/slip condition are considered where the material at the proximity of the FSW tool slips on the lower pressure regions. A right-handed one-way thread on a tilted FSW tool pin with a smooth, concaved shoulder is, additionally, considered to increase the accuracy of the numerical model. In addition, the viscous and frictional heating are assumed as the only sources of heat input. In the course of model verification, good agreements are found between the numerical results and the experimental investigations.