A new design methodology for the vibration control of rotor systems with a magnetic bearing is developed in this paper. The methodology combines the experimental design method in quality control engineering and the conventional PD control technique such that their advantages in implementation feasibility and performance-robustness can be integrated together. A quality loss index defined by the summation of the infinity norm of unbalanced vibration is used to characterize the system dynamics. By using the location of the magnetic bearing and PD feedback gains as design parameters, the controller of experiment-aided design achieves the best system performance. In addition, it is robust to operating speed variations. A rotor system consisting of 4 rigid disks, 3 isotropic bearings, and 1 magnetic bearing is applied to illustrate the feasibility and effectiveness of the experiment-aided controller design.