In recent years, electronic power transformer (EPT), which is also called solid state transformer, has attracted great interest and has been used in place of the conventional power transformers. These transformers have many important functions as high unity power factor, low harmonic distortion, constant DC bus voltage, regulated output voltage and compensation capability. In this study, proposed EPT structure contains a three-phase pulse width modulation rectifier that converts 800 V-rms AC to 2000 V DC bus at input stage, a dual active bridge converter that provides 400 V DC bus with 5:1 high frequency transformer at isolation stage and a three-phase two level inverter that is used to obtain AC output at output stage. In order to enhance dynamic performance of EPT structure, neuro fuzzy controllers which have durable and nonlinear nature are used in input and isolation stages instead of PI controllers. The main aim of EPT structure with the proposed controller is to improve the stability of power system and to provide faster response against disturbances. Moreover, a number of simulation results are carried out to verify EPT structure designed in MATLAB/Simulink environment and to analyze compensation ability for voltage harmonics, voltage flicker and voltage sag/swell conditions.