In this study, the performance of a newly proposed smart base isolation system employing Magneto-Rheological Elastomers (MREs) is numerically evaluated. The MREs are the smart material of which elastic modulus and stiffness can be changed by applying magnetic field to them. To verify the efficacy of the proposed MRE-based isolation system, an extensive numerical simulation study has been performed using a six degree-of-freedom structure under several historical earthquake excitations. The results show that the proposed system could successfully improve the seismic performance of base-isolated structures.