The third generation of Al-Li 2050-T84 alloy was primarily used in aerospace industries due to its exceptional potential for weight saving, high strength, and increased fatigue crack growth resistance. In the present research, three different types of tool pin profiles, namely, hybrid, taper threaded, and triangular, were used to join 2050-T84 Al-Li alloy by using Friction Stir Welding (FSW) at a constant rotational speed of 23.33 rotation/second with a traverse speed of 0.003 meters per second and tilt angle of 2°. The research explored the effect of different tools on weld bead structure, waviness and natural frequency of welded plates. The experimental results show that the hybrid tool pin side generates 10.9% higher heat than the threaded taper tool and 25.8% higher than the triangular tool. Moreover, the hybrid tool produces 50.1% lower waviness of welded specimens than the threaded taper tool and 55.7% lower than the triangular tool at the nugget zone (NZ). The research established that a hybrid tool pin profile is advantageous as it generates a higher frequency and lower acceleration under the applied load in friction stir welded specimens.