This paper addresses the compensation of the vibration caused by flow disturbance, which is the pressure fluctuation of compressed air supplied to a pneumatic anti-vibration apparatus (AVA). The pressure of the compressed air changes periodically during compression process. For this reason, proportional-integral-sinusoidal (PIS) control is utilized so that the flow disturbance can be attenuated. In this control method, a Sinusoidal compensator (S compensator) provides a periodic control input signal whose frequency is the same as the frequency of the disturbance. However, when the PIS control is applied to the vibration attenuation for the pneumatic AVA, there arise two practical problems that have to be solved. First, the vibration of an isolated table occurs in transient state at the start-up/shut-down of the S compensator. This is due to the switching of the S compensator. To deal with the first practical problem, soft switching approach is presented. Second, high-frequency vibration is observed in steady state after the S compensator is started up. Since the source of the high-frequency vibration is the phase-lag of the S compensator, a phase-lead type PIS compensator is employed. By using this compensator, the phase margin of a control system can be increased and the high-frequency vibration can be attenuated. Moreover, in this paper, vibration transmissibility is analyzed so as to investigate effects of the PIS control on the isolation from floor vibration. It is shown that 1) when the PIS control is used, anti-resonance and resonance are excited and 2) there is a trade-off between flow disturbance attenuation and vibration transmissibility reduction.