The dynamic response of flexible five-story building supported on the variable frequency pendulum isolator (VFPI) under bi-directional near-fault ground motions is investigated. In order to verify the effectiveness of the VFPI, the seismic responses are compared with the friction pendulum system (FPS) and variable friction pendulum system (VFPS). The response of the system with bi-directional interaction is compared with those without interaction in order to investigate the effects of bi-directional interaction of frictional forces. Moreover, a parametric study is carried out to critically examine the influence of important parameters on bi-directional interaction of the frictional forces of the VFPI. From the above investigations, it is concluded that under bi-directional near-fault ground motions, the isolator displacement in the VFPI is more than that of the VFPS and the FPS whereas the top floor absolute acceleration and the base shear are less than that of the VFPS and the FPS. Furthermore, if the bi-directional interactions of frictional forces of the VFPI are ignored, the isolator displacements will be under predicted and superstructure acceleration and base shear will be over predicted.