Recently, as large structures such as high-rise building and long span bridge become lighter and more flexible, the necessity of structural control for reducing excessive dynamic response due to seismic excitation is increased. In this study, a semi-active base isolation system using Magneto-Sensitive (MS) rubbers is proposed to effectively protect structures against earthquakes. MS Rubber is a class of smart controllable materials whose mechanical properties change instantly by the application of a magnetic field. To demonstrate the performance of this device, the MS Rubber isolation system is compared to Lead-Rubber Bearing (LRB) isolation systems and judged based on computed responses to several historical earthquakes. The MS Rubber isolation system is shown to achieve notable decreases in base drifts over comparable passive systems with no accompanying increase in base shears or in accelerations imparted to the superstructure. The proposed MS Rubber system is shown to perform better than the passive isolation system.