In this study, the fatigue behaviour of Al–Mg–Si aluminium alloy joints joined by friction stir spot welding (FSSW) was investigated. FSSW was performed using a specially designed double-acting tool consisting of outer flat shoulder and inner retractable probe, which could re-fill probe hole of the joints. Lap-shear specimens with probe hole and re-filled one were fabricated. The tensile strength of the joint with re-filled hole was higher than that of the joint with probe hole, where shear fracture through the nugget occurred in both joints. The re-filling process increased effective cross sectional area of the nugget, resulting in higher tensile strength. Fatigue tests were conducted using lap-shear specimens at a stress ratio of R = 0.1. The fatigue strength of the joint with re-filled probe hole was nearly the same as, but lower than, at low and high applied loads, respectively, that of the joint with probe hole. The pull out of the nugget, i.e., plug type fracture, was seen in the joint with re-filled probe hole, while shear fracture through the nugget was observed in the joint with prove hole. The observation of fatigue crack growth path revealed that the plug type fracture through the upper sheet was responsible for the observed lower fatigue strength of the joint with re-filled prove hole at high applied loads.