The pneumatic vibration isolator is economical, has no risk of contamination, and attains high vibration isolation performance by lowering the natural frequency. Pressure feedback control is used to improve the response speed of the pneumatic vibration isolator and keep the internal pressure of the pneumatic actuator constant. In this paper, the vibration isolator was actively controlled by estimating the internal pressure of the pneumatic actuator with the displacement signal. A pneumatic actuator was modeled and its dynamic characteristics were identified through frequency response measurements. A pressure observer based on relative displacement was designed, and the observer control gain was adjusted with nominal model and experiments. Pressure estimation performance and active vibration suppression performance using a pressure observer were verified through experiments. The pressure of the pneumatic actuator was estimated by the observer, and measurement noise was eliminated effectively. In addition, vibration isolation performances of direct and estimated pressure feedback showed no difference, verifying the effectiveness of the pressure observer.