A technique is introduced to achieve transient vibration attenuation in a multi-input, multi-output flexible rotor/magnetic bearing system. The strategy employs feedback control of measured harmonic components of rotor vibration. Whereas previous harmonic controllers have been based only on steady state vibration characteristics, the new controller also incorporates the transient dynamics. The controller may still be designed from measured data and is determined from target transient vibrational responses arising from step changes in particular disturbances. Account is taken of delays arising from evaluation of harmonic components. Furthermore, stability boundaries for the controller are shown to have significant tolerance to measurement error. The controller is validated experimentally in a flexible rotor/magnetic bearing system and mass loss tests are used to demonstrate rapid decrease in vibration levels with near elimination of transient overshoot.