Wireless power transfer (WPT) is a promising technology and has attracted many researchers’ attention due to its inherent advantages such as reliability, safety, flexibility, and low maintenance costs. For WPT systems, the output voltage varies according to the variable loads and the coupling coefficient conditions, affecting system stability and efficiency. In this regard, this study is concerned with the tracking control problem of WPT systems based on fuzzy supervisory proportional–integral (PI) controller and a phase shift modulation technique, which is for the first time proposed by this paper. By introducing appropriate fuzzy rules, the proposed control scheme not only can track the desired output voltage but also has better robust behaviour to deal with the problem of variations of circuit elements and coupling coefficients. That is, the proposed fuzzy supervisory PI control scheme can perform better than the traditional PI controller. Analysis of the designed control method and simulation results validate the superiority of the proposed method over the traditional PI controller in all conditions, which can make it a suitable choice for the applications of electric vehicle charging systems. The analysis is supported by experimental measurements.