This study compares the performance of two smart isolation systems that utilize superelastic shape memory alloys (SMAs) for seismic protection of bridges using energy balance concepts. The first isolation system is a SMA/rubber-based isolation system (SRB-IS) and consists of a laminated rubber bearing that decouples the superstructure from the bridge piers and a SMA device that provides additional energy dissipation and re-centering capacity. The second isolation system, named as superelastic-friction base isolator (S-FBI), combines the superelastic SMAs with a flat steel-Teflon bearing rather than a laminated rubber bearing. Seismic energy equations of a bridge structure with SMA-based isolation systems are established by absolute and relative energy balance formulations. Nonlinear time history analyses are performed in order to assess the effectiveness of the isolation systems and to compare their performance. The program RSPMatch 2005 is employed to generate spectrum compatible ground motions that are used in time history analyses of the isolated bridge. Results indicate that SRB-IS produces higher seismic input energy, recoverable energy and base shears as compared to the S-FBI system. Also, it is shown that combining superelastic SMAs with a sliding bearing rather than rubber bearing significantly reduce the amount of the required SMA material.