Friction stir spot welding (FSSW) is a solid state joining technology that has the potential to be a replacement for processes like resistance spot welding and rivet technology in certain applications. To optimize the process parameters and to develop FSSW tools, it is important to understand the physics of this complex process that involves frictional contact, high temperature gradients, and large deformations. This paper presents a fully coupled thermo-mechanical finite element model (FEM) model of the plunge phase of a modified refill FSSW. The model was developed in Abaqus/Explicit and the simulation results included the temperature, deformation, stress, and strain distributions in the plates being joined. An experimental study was also conducted to validate the temperatures predicted by the model. The simulation results were in good agreement with the temperatures measured in the experiment. Also, the model was able to predict in a reasonable fashion the stresses and plastic strains in the plates.