This paper presents a comprehensive study on the application of the MR damper to base-isolated building structures. It first proposes a simple semi-active control algorithm for a base-isolated structure with an MR damper. The algorithm, in which the MR damper's hysteresis shape is controlled, aims to reduce the isolator's displacement without increasing the acceleration responses of the upper structures. The second part of this paper covers the properties of an MR fluid and an MR damper developed for a base-isolated model structure. The damper has a nominal capacity of 40kN, which can be adjusted in accordance with the applied magnetic fields. In the test, the damper is subjected to cyclic sinusoidal displacements with different amplitudes, velocities and magnetic field intensities. The last part describes shaking table tests carried out using the MR damper and the base-isolated model structure. It is confirmed that the proposed semi-active control method is effective in reducing the isolator's displacement without increasing the acceleration responses.