A novel method for transient rotor/active magnetic bearing control using sampled wavelet coefficients is proposed. Control currents are formulated in the wavelet transform domain, prior to signal reconstruction. The wavelet based controller is designed from target transient responses due to step changes in wavelet coefficients of applied forces. Transient system dynamics are embedded in the controller and evaluated from on-line system identification. Experimental validation is undertaken using a flexible rotor/active magnetic bearing system. Mass loss tests were performed at two critical speeds corresponding to near sudden changes in unbalance that are capable of exciting rotor dynamic modes in a transient manner. The controller is shown to suppress the transient responses within a finite settling time.