The pressure of air supplied to pneumatic anti-vibration apparatuses (AVAs) varies periodically. It leads to the vibration of an isolated table. This paper focuses on the suppression of the vibration caused by the pressure variation, which is called flow disturbance. Since the flow disturbance is periodic, repetitive control is employed. The time delay in the repetitive controller is determined by considering the variation of the period of supplied air pressure. When the tunable parameter of the repetitive controller is a large constant gain, the performance of disturbance suppression is improved, whereas the transmissibility increases in high frequency region. To avoid the increase of the transmissibility, a dynamic compensator is selected as the tunable parameter instead of the constant gain. It is shown that a notch filter is the dynamic compensator suitable for the improvement of both the transmissibility and the flow disturbance suppression.