A new controller based on a fractional-order synergetic controller (FOSC) is proposed for a three-level T-type inverter using a shunt active power filter (SAPF). The SAPF is designed to compensate for the reactive power and eliminate the current harmonics caused by non-linear loads, in cases of distorted or unbalanced source voltages. The proposed FOSC technique with the designed parameters and defined macro-variable is a robust control technique that operates well in both transient and steady-state scenarios, ensuring fast convergence and closed-loop system stability. The FOSC technique utilizes a phase-locked loop (PLL) technique on a self-tuning filter (STF) to enhance the SAPF’s ability to compensate current harmonics and reactive power in all situations involving non-linear loads and source voltage variations according to IEEE Std. 519. The proposed control was implemented and verified using Matlab software, where the obtained results were compared with the results of the conventional control based on proportional-integral (PI) controllers in different operating conditions. The results indicate that the proposed FOSC technique outperformed the traditional control in terms of DC voltage tracking and the minimization of the total harmonic distortion of the current.