This paper is concerned with the design and implementation of magnetic damper system to reduce the vibration of suspension system actively. Cylindrical type electro-magnetic actuator with permanent magnet is analyzed and effective controller design is made. Magnetic force analyzed and transfer function for the total system is determined by experimental data using error minimization method. For experiments, simple suspension structure system is utilized, in which a magnetic damper composed of permanent magnet and digital controller is attached. In order to drive the system, bipolar power amplifier of voltage control type is utilized. Stable and high speed control board is used to perform digital control logic for the given system. This paper shows that the magnetic damper system using phase-lead controller excellently reduces vibration of 1-D.O.F (degree of freedom) suspension system.