High voltage pulse transformers have an essential role in pulsed power systems and power conversion applications. Improving the electromagnetic behavior of such devices leads to better efficiency and low-level electromagnetic interference (EMI) noise propagation in systems. In this paper, a high voltage pulsed power system is considered and analyzed to improve their electromagnetic compatibility (EMC). The new generation of pulsed power systems that use SiC and GaN fast switches in capacitor charger power electronic circuits, face far more EMI challenges. Moreover, in this paper, the EMI propagation paths in the pulsed power system are realized and analyzed. The EMI noise level of the system is obtained and compared to the IEC61800-3 standa...