A finite control set model predictive control (FCS-MPC) based controller has a fast dynamic response and robustness. furthermore, the presence of a cost function gives designers a degree of freedom to include system control targets, constraints and system non-linearities. On the other hand, Multilevel inverter (MI) topologies are becoming a strong alternative in distributed power generation system (DPGS), among these topologies is the three-phase three-level NPC (TTLNPC) inverter. Generally, to properly operate this topology, the applied current control ensures the achievement of two main objectives. First, the output current must be controlled to track its reference. Second, the two dc-link capacitor voltages have to be equal and balanced. In this paper, FCS-MPC is proposed to control the TTLNPC inverter based parallel active power filter (APF) adopted to connect a photovoltaic system (PVS) to the grid and perform a harmonic mitigation. The proposed FCS-MPC exploit the model of the system to predict the future values of the inverter currents by selecting the best voltage vector that aims to minimize a predefined cost function. Instead of using the popular redundant vectors algorithms to balance the two-split dc-link capacitor voltages, another term will be added to the expression of the cost function to achieve this goal. The PV panel is coupled directly to the inverter without DC/DC converter, the P&O MPPT algorithm is responsible to generate the capacitor reference voltage whatever the climatic conditions are. Simulations using Matlab/Simulink were performed to prove the efficiency of the proposed technique to mitigate the grid current harmonics, and to ensure a continuous power injection and perform a load power sharing.