Active control is regarded as one of the most efficient and economic countermeasures to reduce excessive vibration of ship superstructure. However, it is difficult to find its practical application in real ships in spite that many studies on such systems have been done. In this study, for the practical use of an active control system to reduce ship superstructure vibration, we have developed an active vibration compensator consisting of a mechanical actuator having compact size and expected lifetime over 20 years, its control panel including exclusive signal processing and computing board, sensors to detect phase and vibration, and its operation software providing various user-interface functions. From the performance verification test of the system at a 5,500 TEU container carrier, we have confirmed the system could reduce ship superstructure vibration of a harmonic component of main engine rotating frequency up to 0.1 mm/s.