Nowadays medium voltage conversion systems, like traction and energy distribution systems, aim to increase power density. Volume, weight and material reduction are gaining the market today. Due to the development of new high power semi-conductor devices a new working frequency range is conceived, where magnetic component reduction is feasible. However, along with the reduction of magnetic component size, the cooling surface is reduced, increasing the equilibrium temperature of the magnetic components. The core element of these new conversion systems is the medium frequency power transformer. In this paper a dynamic thermal model is introduced, with equivalent non-linear temperature dependent thermal resistances. Besides, heat sources are determined taking into account non-sinusoidal excitations, and frequency dependent effects. For our case study, the model shows natural heat dissipation limits, pointing out the cooling requirements throughout the design process.