Friction stir welding is a promising solid-state joining process to weld light materials like aluminum alloys. In this paper, an attempt has been made to optimize the friction stir corner welding process parameters using Taguchi grey relational analysis to attain the improved mechanical properties of dissimilar thickness AA5086 and AA6061 dissimilar aluminum alloys with plate thicknesses of 6 mm and 4 mm, respectively. The input parameters of the welding play a crucial role to achieve the desired weld properties. The friction stir welding experiments were conducted according to the L9 orthogonal array. The input process parameters are tool rotation speed (900–1100 r/min), welding speed (100–190 mm/min), and plunge depth (0.1–0.3 mm). The processes parameters were optimized and ranked based on the results of the grey relational analysis. The percentage contribution of each input process parameter on the weld quality was quantified using analysis of variance (ANOVA). The optimal process parameters were determined at tool rotation speed of 1100 r/min, welding speed of 150 mm/min, and tool plunge depth of 0.2 mm. The percentage contribution of the welding speed was 40.50% and revealed a significant influence on multiple responses followed by plunge depth 25.84% and rotational speed 18.13%. The microstructures of various regions were observed and analyzed. The fracture mode and fracture surface of the welded sample were observed and discussed. © IMechE 2018.