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A five-level flying-capacitor (FC)-based active-neutral-point-clamped (ANPC) converter is an arrangement of a three-level ANPC converter and a two-level cell. In this paper, a control strategy is proposed to regulate the voltage across the FCs at their respective reference voltage levels by swapping the switching patterns of the switches based on the polarity of the output current, the polarity of the FC voltage, and the polarity of the fundamental line-to-neutral voltage under selective harmonic elimination pulsewidth modulation. The voltage across the FCs and the dc-link capacitors are simultaneously controlled at their reference voltage levels. The proposed control strategy is applied using power system computer aided design/electromagnetic transients including dc on a static synchronous compensator operating under a power-factor-correction mode to verify its performance. Experimental results are also presented for low and high number of angles per quarter period using a low-power laboratory prototype.