Nanoindentation test was employed to measure the actual hardness and yield strength of the stir zone in the friction stir-welded single-phase brass joints. For this aim, different joints were prepared according to an experimental matrix based on the central composite rotatable design. In this design matrix, the tool rotational speed, tool traverse speed, and tool axial force were the input parameters. The outputs were the hardness and yield strength of the joints. To measure the hardness and tensile strength of the joints, the nanoindentation test was employed. Moreover, electron back scattered diffraction and transmission electron microscopy techniques were used to study the microstructural features. The results showed that by decreasing rotational speed and axial force, and by increasing the traverse speed, the hardness and yield strength of the joints were increased. In other words, lower heat inputs caused higher strength in the joints. Finer grain sizes, larger grain average misorientation amounts, i.e., existence of more dislocations, and greater Taylor factors in the lower heat input joints revealed that the influence of grain boundaries, dislocations, and texture were the origins of better mechanical properties.