Silicon-carbide (SiC) devices are receiving popularity for high-power converter systems in aircraft due to many advantages over silicon counterparts. However, the electromagnetic interference (EMI) problems are more serious with the SiC devices operating at higher switching speeds and higher switching frequencies. The common-mode (CM) EMI filter design of the high-power SiC converter is especially challenging for high-altitude applications due to the harsher requirements of insulation and heat dissipation. The optimization of the parameters and physical design of a CM EMI filter in a 100-kW SiC inverter/rectifier system operating at 50 000 ft is conducted in this article to obtain the highest power density. The effect of the switching frequency on the EMI filter volume and the total power density of the converter system is analyzed. The lower breakdown voltage of air and the higher thermal resistance of natural convection make the conventional design of the CM choke infeasible at high altitudes. A printed circuit board (PCB)-based planar CM choke is designed with the consideration of partial discharge (PD) and heat dissipation at the altitude of 50 000 ft. The structure of the CM choke is optimized with embedded electric-field shielding plates, which controls the electric-field intensity in the air below 300 V/mm. The PCB windings improve the efficiency of heat dissipation at high altitudes and reduce the profile of the CM choke. A Pareto optimization is conducted to minimize the size of the choke and the volume of the final design is only 155 cm3. The experimental results show that the CM noise is reduced effectively with the CM EMI filter. PD is not observed even at the altitude of 50 000 ft and the thermal performance is excellent with a current of 190 A. With the optimization and the dedicated design of the CM EMI filter, the power density of the converter system is up to 33.3 kW/L.