In this paper, we are concerned with the output reference signal tracking for a one dimensional Schrödinger equation subject to general harmonic disturbance at one end and the control at the another end. Based on the reference signal, we design a state reference system and the output feedback control to cancel the disturbance and track the output reference signal. We show that the whole closed‐loop system is well‐posed and the performance output is tracking the reference signal. The numerical experiments are carried out to illustrate the approach effective.