Friction stir welding using the tools with polygonal pins is often found to improve the mechanical strength of weld joint in comparison to the tools with circular pins. However, the impacts of pin profile on the peak temperature, tool torque and traverse force, and the resultant mechanical stresses experienced by the tool have been rarely reported in a systematic manner. An estimation of the rate of heat generation for the tools with polygonal pins is challenging due to their non-axisymmetric cross-section about the tool axis. A novel methodology is presented to analytically estimate the rate of heat generation for the tools with polygonal pins. A three-dimensional heat transfer analysis of friction stir welding is carried out using finite element method. The computed temperature field from the heat transfer model is used to estimate the torque, traverse force and the mechanical stresses experienced by regular triangular, square, pentagon and hexagon pins following the principles of solid mechanics. The computed results show that the peak temperature experienced by the tool pin increases with the number of pin sides. However, the resultant maximum shear stress experienced by the pin reduces from the triangular to hexagonal pins.