Shunt active power filters (SAPF) play a vital role in power systems. Integration of renewable energy sources and electrical vehicle (EV) charging stations proliferate in the modern power system. In such scenario, SAPF is an efficient method for improving power quality. The article suggests a SAPF with multilevel cascaded H-bridge inverter using the instantaneous real and reactive power (P–Q) theory based control technique to derive reference currents for the compensation unit from active and reactive power to suppress harmonics present in the power system. The conventional-proportional integral (PI) and intelligent-fuzzy logic controller (FLC) were used as voltage controllers for maintaining the DC link voltage. The article proposed an aggregated PWM signal-switching circuit for balancing the individual capacitor voltage. The proposed system harmonic results are compared with conventional triangular PWM and aggregated PWM. The proposed switching circuit balanced the individual capacitor voltage and minimized the total harmonic distortion (THD) in the sinusoidal source voltages and currents. Simulation and prototype results reveals that proposed aggregated PWM system with FLC dominates the conventional PI controller.