The vibration suppression on a resonant system, based on the reflected wave rejection, has been recently proposed. In the method, the resonant system is modeled through a wave equation, in order to consider high order vibrations and vibration suppression is achieved by eliminating a reflected wave from the resonant system. However, it is impossible to implement such method when there are input and output time delays, because it would require the implementation of the inverse of a time delay. This paper proposes a new vibration suppression scheme for a resonant systems, affected by time delay, by using a modified reflected wave rejection. The proposed reflected wave rejection can be applied even in presence of time delays, as long as some conditions on the value of such delays are satisfied. The validity of the proposed method is confirmed by simulations and experimental results.