This paper presents a simultaneous synthesis method of both motion and vibration controllers using a frequency-shaped time-varying criterion function for the positioning problem of flexible structures. In order to improve the efficiency control and the robustness of the control, in this method, the characteristic difference in frequency range between positioning and vibration controls is taken into consideration and different frequency-shaped weightings are individually performed for the positioning and the vibration reduction. In comparison with the time-optimal control, the control input derived from this criterion function shows similar characteristics in the frequency domain. This method is applied to a positioning control problem of a positioning model with a vibration system and is compared with the optimal control using a time-varying criterion function without frequency-shaping. The appropriateness of this method is verified by numerical analysis.