A new control technique known as inverted error deviation (IED) control is incorporated into the main DC-link capacitor voltage regulation algorithm of a three-level neutral-point diode clamped (NPC) inverter-based shunt active power filter (SAPF) to enhance its performance in overall DC-link voltage regulation so as to improve its harmonics mitigation performances. In the SAPF controller, DC-link capacitor voltage regulation algorithms with either the proportional-integral (PI) or fuzzy logic control (FLC) technique have played a significant role in maintaining a constant DC-link voltage across the DC-link capacitors. However, both techniques are mostly operated based on a direct voltage error manipulation approach which is insufficient to address the severe DC-link voltage deviation that occurs during dynamic-state conditions. As a result, the conventional algorithms perform poorly with large overshoot, undershoot, and slow response time. Therefore, the IED control technique is proposed to precisely address the DC-link voltage deviation. To validate effectiveness and feasibility of the proposed algorithm, simulation work in MATLAB-Simulink and experimental implementation utilizing a TMS320F28335 Digital Signal Processor (DSP) are performed. Moreover, conventional algorithms with PI and FLC techniques are tested too for comparison purposes. Both simulation and experimental results are presented, confirming the improvement achieved by the proposed algorithm in terms of accuracy and dynamic response in comparison to the conventional algorithms.