The medium frequency transformer (MFT) with nanocrystalline alloys is quintessential in new DC–DC converters involved in various front-end applications. The center piece to achieve high-performance, efficient MFTs is the core. There are various options of core materials; however, no deep information is available about which material characteristics and design procedure combo are best to get high performance MFTs while operating at maximal power density. To provide new insights about interrelation between the selection of the core material with the compliance technical specifications, differently to other proposals, this research work aims to design and build, with the same methodology, two MFT prototypes at 20 kHz, with nanocrystalline and ferrite cores, to highlight power density, and overall performance and cost, as matching design criteria. As the experimental results show, a nanocrystalline core has the highest power density (36.91 kW/L), designed at 0.8 T to obtain low losses at 20 kHz, achieving an efficiency of 99.7%. The power density in the ferrite MFT is 56.4% lower than in the nanocrystalline MFT. However, regarding construction cost, the ferrite MFT is 46% lower, providing this a trend towards low-cost DC–DC converters. Finally, high power density in MFTs increases the power density of power DC–DC converters, which have relevant applications in fuel cell-supplied systems, renewable energies, electric vehicles, and solid-state transformers.