This paper presents a control system for active magnetic bearings (AMBs) considering the motions of the stator. AMBs require active control for stable support of the rotor. Many control methods for AMBs have been proposed. Most of them are designed with no regard to the stator motions because the stator is usually fixed on the base. However, in some applications, the stator moves with the object in which the AMB is mounted. In this paper, the influences of the stator motions on the relative angle of the rotor to the stator are investigated both theoretically and experimentally. In addition, the signals estimated by a disturbance observer are used to compensate the influences. The influences become remarkable at a low frequency range. The upper side of the remarkable range extends to higher frequency range when the gyroscopic effect is large. The influences are cancelled by the compensation using the observer. The effect of the cancellation depends on the estimation speed of the observer.