Real-time hybrid simulation (RTHS) is a versatile, effective, and promising experimental method used to evaluate the structural performance under dynamic loads. In RTHS, the emulated structure is divided into a numerically simulated substructure (NS) and a physically tested substructure (PS), and a transfer system is used to ensure the force equilibrium and deformation compatibility between the substructures. Owing to the inherent dynamics of the PS and transfer system (referred to as a control plant in this study), there is a time-delay between the displacement command and measurement. This causes de-synchronization between the boundary of the PS and NS, and affects the stability and accuracy of the RTHS. In this study, a Kalman filter-based adaptive delay compensation (KF-ADC) method is proposed to address this issue. In this novel method, the control plant is represented by a discrete-time model, whose coefficients are time-varying and are estimated online by the KF using the displacement commands and measurements. Based on this time-varying model, the delay compensator is constructed employing the desired displacements. The KF performance is investigated theoretically and numerically. To assess the performance of the proposed strategy, a series of virtual RTHSs are performed on the Benchmark problem in RTHS, which was based on an actual experimental system. Meanwhile, several promising delay-compensation strategies are employed for comparison. Results reveal that the proposed time-delay compensation method effectively enhances the accuracy, stability, and robustness of RTHS.