Harmonic currents in active magnetic bearing systems are caused by rotor imbalance and sensor runout, which consequently result in harmonic vibrations. Repetitive controller can suppress both same frequency and multiply frequency harmonics, but traditional repetitive controller must satisfy that the control system sampling frequency is an integer multiple of the actual rotor speed, which severely limits their applicability. To solve this problem, an improved dual mode fractional order repetitive controller is designed. The Lagrange interpolation method is utilized to convert the fractional order to an integer, addressing the non-integer delay issue in repetitive control. Even and odd harmonics are independently suppressed through dual channels, the 1st, 2nd, 3rd, 4th and 5th harmonics are respectively reduced by 87.9%, 61.3%, 86.9%, 36.9% and 85.3%. Simulation and experimental results verify the accuracy and effectiveness of the improved repetitive controller for harmonic current suppression.