The dynamic behavior of a pile-supported structure with a base isolator was investigated by using 1 g shaking table model tests considering soil–structure interaction (SSI). The emphasis was placed on evaluating the effect of the with/without developed base isolator on the dynamic behavior of end-bearing piles and structures. The experiment was performed through sweep tests and sinusoidal wave tests. As a result of the tests, the developed base isolator was found to effectively reduce the structure’s resonant frequencies and damped the response acceleration under resonance frequencies. According to sweep tests, the base shear force of the pile-supported structure system tends to decrease as the relative density of the soil increases during resonance. It showed that the base isolator tends to reduce significantly the response acceleration of not only the rigid-based structure but also the pile-supported structure. It was shown that although the isolated superstructure recorded large horizontal displacements, piles experienced reduced horizontal displacement and bending moments, regardless of soil conditions.