Along with the rapid advances in power electronics and semiconductor technology, electronic power transformers (EPTs), which are expected to replace conventional power transformers in the future, are being developed and designed. This study presents the dynamic performance of the intelligent controller structure in the control of an EPT. The EPT structure, consisting of the input, isolation, and output stages, is designed for experimental and simulation studies. A three-phase pulse width modulation (PWM) rectifier is used to rectify the grid voltages at the input stage of EPT. The DC-bus voltage of the three-phase PWM rectifier is controlled by a neuro-fuzzy controller (NFC) against the disturbances that may occur in the input stage. In the isolation stage of the EPT, a DC-DC converter circuit is used. Thus, DC voltage obtained from the input part is reduced to the appropriate voltage values. In the output stage, the two-level three-phase inverter circuit is used to provide the necessary voltages for users. The control algorithms for input and output stages of the EPT have been developed using a dSPACE DS1104 controller card, which can work in real time with MATLAB/Simulink. Experimental and simulation studies are realized to demonstrate the voltage sag, swell, harmonic, and reactive power compensation performances of the EPT controlled by NFC.