The microstructures, tensile shear properties, and tensile shear fatigue properties of dissimilar A6061/Galvannealed steel joints fabricated by friction stir spot welding (FSSW) were investigated. Fe4Al13 phases form as the intermetallic compound (IMC) layer at the joint interface between the A6061 matrix and the galvannealed layer consisting of FeZn7, Fe, and Zn. At the edge of the joint, the stirred layer in which the A6061 matrix and the galvannealed layer are stirred also forms. Moreover, the solidified part of the residual melt discharged from the joint area forms at the outer peripheries of the joint. In this study, FSSW was conducted for two total welding durations: 9 and 10 s. Although the thickness of the remaining A6061 sheet in the welded area decreased with an increase in the welding time, the effects of the total welding time on tensile shear and tensile shear fatigue properties were negligible. A fatigue fracture occurred in the A6061 matrix and at the joint interface at the high cycle fatigue region and the low cycle fatigue region, respectively. In the case of the interfacial fracture, the crack was generated in the solidified part of the residual melt or at the interface between the solidified part and the stirred layer.