This paper addresses the compensation problem of flow disturbance and floor vibration for pneumatic vibration isolators. In the proposed method, repetitive control is applied in order to attenuate the flow disturbance. When the tunable parameter of a repetitive controller is selected as high-gain static compensator, the performance of flow disturbance attenuation can be improved. However, in this approach, peak transmissibility increases. It leads to the performance degradation of floor vibration attenuation. In order to balance the trade-off between the flow disturbance attenuation and the peak transmissibility reduction, a phase-lag type dynamic compensator is adopted as the tunable parameter of the repetitive controller. Simulation and experimental results show that the effects of flow disturbance can be compensated and the transmissibility can be improved by means of the proposed method.