The active magnetic bearing (AMB) systems mounted in moving vehicles are exposed to the disturbances due to the base motion, often leading to malfunction or damage as well as inaccurate positioning of the systems. Thus, in the controller design of such AMB systems, robustness to base disturbances becomes an essential requirement. In this study, effective control schemes are proposed for the homo-polar AMB system, which uses permanent magnets for generation of bias magnetic flux, when it is subject to base motion, and its control performance is experimentally evaluated. The base motion of AMB system is modeled as the dynamic disturbances in the gravity and base excitation forces. To effectively compensate for the disturbances, the angle feed-forward controller based on the inverse dynamic model and the acceleration feed-forward controller based on the normalized filtered-X LMS algorithm are proposed. The performance test of the prototype AMB system is carried out, when the system is mounted on rate table. The experimental results show that the performance of the proposed controllers for the AMB system is satisfactory in compensating for the disturbances due to the base motion.