A comparative investigation on rotating bending fatigue behaviour between unnotched and notched specimens of friction stir-welded (FSW) AA6061-T651aluminium alloy joints has been conducted under completely reversed cyclic loading (R = −1). Post-weld aging treatment was done for 8 h at 200°C on the welded joints. After post-weld aging treatment, the fatigue strength was significantly improved, while the grain size remained unchanged. Microstructural evolution before and after post-weld aging treatment was studied using orientation imaging microscopy (OIM) and transmission electron microscopy (TEM). It was found that post-weld aging treatment decreased dislocation density and facilitated precipitation hardening through the reprecipitation of fine β″(Mg2Si) particles. Fine particles of post-weld aged specimens of FSW joints were sheared by dislocations generated during cyclic loading, resulting in difficult crack initiation and tortuous crack propagation. Fractographic results confirmed that Post-weld aged specimens of FSW joints have better fatigue resistance than as-welded specimens, owing to the presence of significant precipitates along the grain boundary.