Active power filters (APFs) are used to mitigate the harmonics generated by nonlinear loads in distribution networks. Therefore, due to the increase of nonlinear loads in power systems, it is necessary to reduce current harmonics. One typical method is utilizing Shunt Active Power Filters (SAPFs). This paper proposes an outstanding controller to improve the performance of the three-phase 25-kVA SAPF. This controller can reduce the current total harmonic distortion (THD), and is called fractional order PI-fractional order PD (FOPI-FOPD) cascade controller. In this study, another qualified controller was applied, called multistage fractional order PID controller, to show the superiority of the FOPI-FOPD cascade controller to the multistage FOPID controller. Both controllers were designed based on a non-dominated sorting genetic algorithm (NSGA-II). The obtained results demonstrate that the steady-state response and transient characteristics achieved by the FO (PI + PD) cascade controller are superior to the ones obtained by the multistage FOPID controller. The proposed controller was able to significantly reduce the source current THD to less than 2%, which is about a 52% reduction compared to the previous work in the introduction. Finally, the studied SAPF system with the proposed cascade controller was developed in the hardware-In-the Loop (HiL) simulation for real-time examinations.