In the last decade, it has been clearly identified that one of the main advantages of friction stir welding (FSW) is to produce sound solid-state joints having mechanical properties comparable to those of the parent material. However, deviations from the appropriated parameters envelope may result in defective welds. Such welds might need to be repaired preferably with the same welding parameters employed for producing defect-free welds. In recent studies, it has been reported that friction stir repaired welds (i.e. RW) achieve fatigue strength comparable to sound welds (i.e. original welds, OW), indicating that the additional thermal cycle and deformation process do not adversely affect the mechanical properties of the joints. In order to understand the effects of repairs on structural integrity and assessment of friction stir welded joints, in the present work, the fatigue behaviour of repair welds subjected to different heat treatment sequences has been investigated. Defective friction stir welded butt joints have been purposely produced on 4 mm thick AA6056-T4. Part of them has been artificially aged before being repaired (i.e. T4-T6-RW). Another batch of defective welds has been repaired and subsequently aged to T6 temper (i.e. T4-RW-T6). Welded samples have been initially undergone microstructural analysis and tensile testing. The determination of fatigue properties has been carried out by means of SN data and fatigue fracture surfaces analysis. T4-T6-RW show a sensible increase in fatigue endurance limit (evaluated at two million of cycles with the probability of 97.7% and the confidence of 95%) when compared with T4-RW-T6, suggesting, as improvement on the mechanical strength of the repaired components, an ageing treatment prior to the repair procedure. Although T4-T6-RW specimens have a fatigue strength higher than that of the parent material, the observed fatigue failure mechanism is comparable to that observed in specimens T4-RW-T6.