Micro Friction Stir Spot Welding (mFSSW) is a welding method on a thin sheet of metal. This welding method is frequently used because of its advantages compared to the other conventional welding method such as RSW. Micro FSSW produced better performance in aluminum alloy with a strong welding joint and longer fatigue life. This research intends to discover the effect of tools geometry on welding joints produced by the mFSSW method using a base material of aluminum alloy 1100 in the form of repetitive load through the dynamic fatigue test. In this research, three different tools were used, where each tool had different pin and shoulder dimensions. The fatigue test was performed on five different loads in each tool. The testing result would be processed and analyzed to create an S–N diagram and failure mode analysis for each specimen to discover which tools geometry has the best endurance against repetitive load. The results showed that Tool 3 (two-step pin), which had a small outer pin diameter and a large shoulder diameter compared to other tools, produced an S–N diagram that fitted the basic theory and had the smallest statistical error. The failure mode generated from all tests was in the form of a nugget pullout.