Substructure shake table testing is a class of real-time hybrid simulation (RTHS). It combines shake table tests of substructures with real-time computational simulation of the remaining part of the structure to assess dynamic response of the entire structure. Unlike in the conventional hybrid simulation, substructure shake table testing imposes acceleration compatibilities at substructure boundaries. However, acceleration tracking of shake tables is extremely challenging, and it is not possible to produce perfect acceleration tracking without time delay. If responses of the experimental substructure have high correlation with ground accelerations, response errors are inevitably induced by the erroneous input acceleration. Feeding the erroneous responses into the RTHS procedure will deteriorate the simulation results. This study presents a set of techniques to enable reliable substructure shake table testing. The developed techniques include compensation techniques for errors induced by imperfect input acceleration of shake tables, model-based actuator delay compensation with state observer, and force correction to eliminate process and measurement noises. These techniques are experimentally investigated through RTHS using a uni-axial shake table and three-story steel frame structure at the Johns Hopkins University. The simulation results showed that substructure shake table testing with the developed compensation techniques provides an accurate and reliable means to simulate the dynamic responses of the entire structure under earthquake excitations.