The solid state friction stir welding (FSW) has been recently the choice for joining of thermoplastics. The present work aims at analyzing the implementation of FSW in joining of different thermoplastics namely, polycarbonate and nylon-6 sheets using varying tool pin profiles, cylindrical, square, and triangular. The novelty of this article is the comparative assessment that has been made on the weldability of these two thermoplastics by determining the mechanical properties of the joint along with real-time acquired force, torque, and temperature signals. Higher axial force with reduced torque has been observed for nylon-6 as compared to polycarbonate. The joint efficiency was found to be maximum (>50%) at tool rotational speed 1800 rpm and welding speed 20 mm/min using square tool pin profile for each of the base materials. Minor undercut defect along with improved material mixing has been seen during the tool stirring process. The study would be helpful for the industries to choose thermoplastics based on their applications.