Base isolation system is widely used for reduction of dynamic responses of structures subjected to seismic load. Recently, research on a smart base isolation system that can effectively reduce dynamic responses of the isolated structure without accompanying increases in base drifts has been actively conducted. In this study, a smart base isolation system was applied to an arch structure subjected to seismic excitation and its control performance for reduction of seismic responses was evaluated. In order to make a smart base isolation system, 4kN MR dampers and low damping elastomeric bearings were used. Seismic response control performance of the proposed smart base isolation system was compared to that of the optimally designed lead-rubber bearing(LRB) isolation system. To this end, an artificial ground motion developed based on KBC2009 design response spectrum was used as a seismic excitation. Fuzzy control algorithm was used to control MR damper in the smart base isolation system and multi-objective genetic algorithm was employed to optimize the fuzzy controller. Based on numerical simulation results, it has been shown that the smart base isolation system can drastically reduce base drifts and seismic responses of the example arch structure in comparison with LRB isolation system.