A thorough understanding of the dynamics of the seismic isolators is essential for evaluating the seismic response of seismically isolated structures. However, the loading tests of full-scale seismic isolators are limited because of the capacity of the testing facilities. Consequently, a new full-scale testing facility—E-Isolation—was built in Japan. The force measurement system using the reaction beam and measurement links is a unique characteristic of E-Isolation; it helps in preventing the contamination of friction and inertial forces of the moving platen. However, the inertial force of the reaction beam can slightly contaminate the measured force in the dynamic loading test. This study aims to establish the force measurement method for E-Isolation considering the dynamics of the testing facility. The impact test is conducted to gain a better understanding of the dynamics of the reaction beam. The dominant frequencies and mode shapes are identified via frequency domain decomposition. The simple force measurement method is proposed based on this result. The lowpass filter is used to simplify the inertial force of the reaction beam. This method also considers the tradeoff between attenuation and phase delay of the filter, and can be applied to real-time hybrid simulation. A verification test is conducted with an oil damper; the results indicate that the proposed method achieves good accuracy in measuring the specimen force. Lastly, dynamic loading tests are conducted on a full-scale seismic isolator for bridges. The result indicates that the equivalent viscous damping of the seismic isolator for bridges is much higher than that for buildings.