In magnetically suspended rotor system, harmonic current mainly originates from rotor mass imbalance and sensor run out, which can generate multi frequency vibration. Repetitive control (RC) is an effective method to eliminate periodic disturbance on a control system. Conventional RC (CRC) requires exact knowledge of the period of the periodic signal. However, in some applications, the period may fluctuate or may not be available with sufficient accuracy, in which case the performance of CRC severely decays. Besides, the transient response of CRC is relatively slow. In response to these issues, a second order RC incorporating dual mode structure scheme is proposed in this project. By introducing Lagrange interpolation based fractional delay filters; the current suppression accuracy gets enhanced in fractional cases. The stability criterion with rigorous proof for the proposed scheme is addressed. The sensitivity to period time of the proposed scheme is analyzed as well from the aspect of sensitivity transfer function. Simulation and experimental validations are performed on a magnetically suspended rotor to show the effectiveness of the proposed approach.