In this paper, a novel tuning strategy for the fractional order proportional integral and fractional order [proportional integral] controllers is proposed for the permanent magnet synchronous motor servo drive system. The tuning strategy is based on a genetic algorithm–wavelet neural network hybrid method. Firstly, the initial values of the control parameters of the fractional order controllers are selected according to a new global tuning rule, which is based on the genetic algorithm and considers both the time- and frequency-domain specifications. Secondly, the wavelet neural network is utilized to update the control parameters based on the selected initial values in an online manner which improves the capability of handling parameter variations and time-varying operating conditions. Furthermore, to improve the computational efficiency, a recursive least squares algorithm, which provides information to the wavelet neural network, is used to identify the permanent magnet synchronous motor drive system. Finally, experimental results on the permanent magnet synchronous motor drive system show both of the two proposed fractional order controllers work efficiently, with improved performance comparing with their traditional counterpart.