The tool pin in friction stir welding experiences fluctuating stresses due to combined bending and torsion because of the simultaneous linear and rotational motions. The resultant bending and shear stresses contribute to the magnitude of the fluctuating stresses experienced by the pin. Here we propose a methodology to estimate the maximum shear stress and the extent of the fluctuating stresses on the tool pins with circular, triangular and square profiles using a three-dimensional heat transfer analysis and solid mechanics based principles. The computed values of thermal cycle and torque are validated with the corresponding measured results. The estimated traverse force is found to be of the similar order of magnitude for FSW of similar materials. For a given welding condition, the tool pin with circular profile experiences the lowest magnitude and the fluctuation of the maximum shear stress.