Smart base isolation systems developed for structures in high seismic regions cannot be directly applied to structures in regions of low-to-moderate seismicity, such as Korea. Therefore, the problems that occur by applying the smart base isolation system for high seismic regions to the structures in regions of low-to-moderate seismicity have been investigated in this study. To this end, a five-story building is used as an example, and an MR damper and low damping elastomeric bearings were used to compose a smart base isolation system. Artificial earthquakes are simulated for ground motions in regions of high and low-to-moderate seismicity. Based on numerical simulation results, the MR damper capacity that can provide good control is quite different among regions of high and low-to-moderate seismicity. Moreover, it is noted that the properties of a smart base isolation system for the regions of low-to-moderate seismicity should be carefully designed because the base isolation effects of the smart base isolation system for high seismic regions deteriorate when it is applied to the structures in regions of low-to-moderate seismicity.