The control of structural vibrations due to ground motion can be done by the installation of a passive, active, and hybrid base isolation system. The primary function of the base isolator is to support the superstructure and provide huge horizontal flexibility and a long period of vibration. In this paper, a special HRDB base isolator is made from natural rubber with special elastic property and hardness. This base isolator is designed to support gravity loads of two-story RC building. The experimental hysteresis loop of this isolator is validated with analytical modeling hysteresis loop using Hysteresis program. The Bouc hysteresis rule was chosen as a model the hysteresis loop, and it is similar to experimental hysteresis loops. Later, a single bay two-story RC frame with a base isolation system was modeled using Ruaumoko 2D program subjected to three levels of earthquake excitations. After analyzing this frame under the 1994 Pacoima Dam Earthquake, the 1995 Kobe Earthquake and the 1940 El-Centro 1940 Earthquake. The numerical results show that this isolator is quite efficient in reducing the damage of structural and non-structural elements of the structure through minimizing inter-story drift, lateral displacement, and story acceleration. Therefore, this special HRDB based isolator is recommended to be used for low rise and medium-rise building in seismic regions.