This paper presents the main experimental evaluation results of SiC MOSFET and GaN FET performance in a 3-phase 3-level neutral point diode clamped inverter prototype. The prototype is built with 650 V class commercially available SiC Schottky diodes and SiC MOSFETs that are replaced and compared with GaN FETs to assess semiconductor device performance in auxiliary converters for transportation application. Inverter variable frequency operation in wide switching frequency range is analyzed for both cases and the acquired results show low switching losses and high efficiency with different input and output parameters. Analysis results approve that despite higher purchase costs, the wide bandgap semiconductor devices can achieve excellent performance in transportation applications, compared to Si IGBTs. High initial price is compensated by reduced losses throughout converter life cycle and, hence, the use of wide bandgap devices is technically and economically effective. Utilization of GaN FETs, compared to SiC MOSFETs, have shown similar experimental results in terms of converter efficiency and loss distribution, but considerably higher initial purchase price and, hence, SiC MOSFETs are approved to be recommended for auxiliary converter design currently because of better price-performance balance.