This paper concerns rotor vibration reduction using magnetic damper system. The fuzzy control logic is utilized to fulfill desired motion. The fuzzy system structure and membership function were first determined by simulation results. The researched control logic contains two fuzzy controller : reference position variation according to the rotor whirling status and error compensation algorithm to minimize the rotor vibration due to unbalance and unstable fluid film force. The Sugeno type output membership function was utilized by several trials and optimized membership function constants were selected from experiments. The experimental results show that the proposed method effectively control and reduce the rotor vibration with fluid film bearings.