Active vibration control methods are required in the high speed rotor systems supported by magnetic bearings. A prediction control technique is one of the control methods. Gain and phase angle are primarily chosen with analyzing the responses for a certain rotor speed. The feasibility of this technique has been reported for only analytical simulations. Therefore this paper constructs the test rig supported by ball bearings with a magnetic bearing type actuator and develops a prediction control system by using LabVIEW and Compact RIO. Finally as rotating speeds are modulated, the gains and phase angles for the speeds are determined with vibration control of the test rig. This leads that the prediction control technique may be applied to the rotor system with the magnetic bearing.