Low-rise masonry building is one of the most commonly adopted structural types even in earthquake prone regions in developing countries. The building is generally susceptible to damage due to earthquake induced motion and may suffer partial or total collapse. Un-bonded fiber reinforced elastomeric isolator (U-FREI) is a relatively new seismic base isolator and is expected to be an attractive option for seismic mitigation of low-rise buildings. In this paper, the effectiveness of a base-isolated masonry building supported on U-FREIs subjected to earthquakes is investigated by finite element (FE) analysis using SAP2000. The prototype building is a two-storey masonry building located at Tawang, Arunachal Pradesh State, India and is the first such U-FREIs supported prototype low-rise building constructed anywhere in the world. Mechanical characteristics of U-FREIs obtained from both experiments and FE analysis are utilized in defining the nonlinear property of the model used for simulating U-FREIs. The force-deformation behaviour of the isolator is modelled as bi-linear hysteretic behaviour, which can be effectively used to model all isolation system in practice. Time history analysis of the building for both fixed-base (FB) and base-isolated (BI) conditions under the action of various recorded real earthquakes are investigated. Comparison of the dynamic response of both FB and BI buildings is computed to evaluate the effectiveness of the base isolation system. The FE analysis results show that floor acceleration and inter-storey drift responses of the BI building under earthquakes are significantly lesser than those of the FB building. U-FREIs are recommended for seismic isolation of low-rise masonry building.