Base-isolated structures achieve superior seismic performance but with the cost of large deformation of the base floor, which possibly causes superstructure collapse during severe earthquakes. Hence, it is of great interest to develop hybrid base isolation systems that can reduce the base deformation and simultaneously improve the superstructure’s performance. Recently, several hybrid base isolation systems using inerter-based dampers have emerged; however, the nonlinear performance of the isolators has rarely been considered in these studies. In this paper, we conduct a nonlinear stochastic optimization of a novel hybrid base isolation system with lead-rubber bearings (LRB) and electromagnetic inertial mass dampers (EIMD). Based on the Bouc–Wen hysteretic model of the LRB, we derive the semianalytical solutions of the response variances of a simplified base-isolated model subjected to stationary seismic excitations. Then, based on the semianalytical solutions, we propose a procedure for optimizing the EIMD aimed at minimizing the superstructure interstory drift. In addition, we investigate the effect of site conditions and postyielding to preyielding stiffness ratios of the LRB on the optimal EIMD parameters and corresponding seismic performance. It is found that the hybrid base isolation system achieves better performance at a soft site than at a firm site. Results of a hybrid base-isolated building under artificial and real earthquake excitations illustrate that the EIMD can reduce both the base deformation and superstructure response, which outperforms the hybrid base-isolated building with conventional viscous dampers (VD).