A modular structured and high efficient photovoltaic (PV) system is essential in today’s scenario. The single stage Cuk based inverter has continuous input and output current, and hence, makes it suitable for applying MPPT techniques when used for PV applications. The PI, PID, and fuzzy controllers could be applied for PV inverter. The PI controller decreases the error in steady state, and at the same time, it also decreases the stability of the system. The PID controller involves large time delay process. The random nature in fuzzy controller may not lead to optimum results. Hence, this paper proposes a controller based on Adaptive Neuro-Fuzzy Inference System (ANFIS) for a three phase PV inverter based on Cuk converter. The effectiveness of proposed system is verified using MATLAB/SIMULINK, and the results are presented. The performance of proposed ANFIS controller for Cuk based three phase inverter is compared with conventional PI controller. The proposed system has several merits like increased performance, accuracy, and efficiency.