In the current scenario, the light-weighting concept is the most important strategy to decrease fuel consumption as well as emissions of greenhouse gases. Magnesium alloys are attractive to various industries including transportation industry for their inherent light-weight. The friction stir welding is proficient to join magnesium alloys. In this article, a dissimilar friction stir welding butt joint between AZ31 and AZ61 magnesium alloys was fabricated, and microstructure and mechanical properties have been examined. The tool rotation speed of 1400 r/min and tool transverse feed rate of 25 mm/min was found quite suitable to fabricate a perfect joint of these dissimilar magnesium alloys. The stir zone was composed of fine and equiaxed grains and showed the highest microhardness value. In the advancing side, heat affected zone was composed of both equiaxed and elongated grains; however, in the retreating side, heat affected zone has relatively smooth grains. The tensile strength of the joint was about 138.37 ± 6.6 MPa. The efficiency of the joint was 51.25% with respect to AZ61 Mg alloy. The average impact toughness of friction stir welding joint was deteriorated by 16.67% and 28.5% with respect to base materials AZ31 and AZ61, respectively.