The real-time hybrid test (RTHT) is designed to predict structural dynamic behavior through the interactions between the physical substructure and numerical model. This study sought to develop the computational algorithm and to optimize the control system with such. Specifically, Finite Element Analysis Program for Hybrid (FEAPH), a nonlinear finite element analysis program for hybrid only, was developed. To shorten the computational time, FEAPH employed the fixed number iteration method and parallel computational technique. Furthermore, in the real-time control system, the inter-communication between a substructure and an analysis program was simplified. To verify the reliability and applicability of the system, nonlinear multi-directional tests of 3DOFs were conducted on a steel frame structure. The RTHT with FEAPH revealed better improvement in terms of testing time and experimental errors. Therefore, the RTHT method using FEAPH can be utilized as an efficient, economical testing method in predicting structural dynamic behaviors.