This study introduces a track-following controller design to measure the rotor dynamics (RD) coefficient of the annular seal using active magnetic bearings. The annular seal is implemented contiguously to prevent leakage of fluid between the rotating shaft and stationary area of a rotating machine. The force caused by the seal at the contact point can cause vibrations, which should be identified for designing rotating machinery. The RD force is coupled with mechanical and fluid dynamics. Moreover, the dynamics depend on the operating conditions of the rotating machine, namely, the rotating speed and orbit of the rotating shaft. This study proposes a control system for the active magnetic bearing to measure the RD force directly at the arbitrary operating condition. The main controller is designed to satisfy a criterion of the frequency characteristics of the rotating system. In addition, the control system employs adaptive feed-forward cancellation (AFC). This can estimate and compensate for the RD force in the control system simultaneously. The experimental results indicate that the control system can achieve an arbitrary operating condition and measure the RD coefficient of the annular seal in real-time. As a result, the RD coefficient is identified based on the equation of motion.