The damaging effects of strong ground motions on highway bridges have revealed the limitations of conventional design methods and emphasized the need for innovative design concepts. Although seismic isolation systems have been proven to be an effective method of improving the response of bridges during earthquakes, the performance of base-isolated structures during near-field earthquakes has been questioned in recent years. Near-field earthquakes are characterized by long period and large- velocity pulses. They amplify seismic response of the isolation system since the period of these pulses usually coincides with the period of the isolated structures. This study explores the feasibility and effectiveness of shape memory alloy (SMA)-based isolation systems in order to mitigate the response of bridge structures against near-field ground motions. SMAs have several unique properties that can be exploited in seismic control applications. In this work, uniaxial tensile tests are conducted first to evaluate the degree to which the behavior of SMAs is affected by variations in loading rate and temperature. Then, a neuro-fuzzy model is developed to simulate the superelastic behavior of SMAs. The model is capable of capturing rate- and temperature-dependent material response while it remains simple enough to carry out numerical simulations. Next, parametric studies are conducted to investigate the effectiveness of two SMA-based isolation systems, namely superelastic-friction base isolator (S-FBI) system and SMA/rubber-based (SRB) isolation system. The S-FBI system combines superelastic SMAs with a flat steel-Teflon bearing, whereas the SRB isolation system combines SMAs with a laminated rubber bearing rather than a sliding bearing. Upon evaluating the optimum design parameters for both SMA-based isolation systems, nonlinear time history analyzes with energy balance assessment are conducted to compare their performances. The results show that the S-FBI system has more favorable properties than the SRB isolation system. Next, the performance of the S-FBI systems is compared with that of traditional isolation systems used in practice. In addition, the effect of outside temperature on the seismic response of the S-FBI system is assessed. It is revealed that the S-FBI system can successfully reduce the response of bridges against near-field earthquakes and has excellent re-centering ability.