Transformers are generally designed to operate under the sinusoidal excitation and the method called classical design method is used in design process. Nevertheless, they have to operate under the partly or fully non-linear excitation because of the increasing amount of the non-linear loads such as rectifiers, electric motor drivers, compact fluorescent lamps, computers, etc. Non-linear loads cause abnormal temperature rise both in the core and in the windings of the transformer which are designed for sinusoidal excitation. Nowadays in the virtual environment provided by the electromagnetic design software, transformers can be easily modeled with the finite element method for any type of non-linear loads or excitations. In this study, 3-D electromagnetic and thermal modeling of the isolation transformer at a certain rated power level have been carried out. Then, the core and the winding temperatures of the transformer have been comparatively reported under the linear and non-linear load conditions. Besides, forced air-cooling method of the transformer has been tested with the CFD. This study has shown that, transformer temperature can be kept in the safe operating region in any type of load by deciding the fan speed providing the required air-flow according to the transformer temperature.