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 standard. To improve the EMC, the parasitic parameters of the transformer, as the main path of EMI circulation, are optimized to block the EMI propagation in the pulsed power system. To achieve this result, the parasitics are modeled and calculated with a novel and accurate energy distribution model. Then, by defining a cost function, the geometry structure of the transformer is optimized to lower the parasitics in the system. Three pareto-optimal techniques are investigated for the cost function optimization. The models and results are verified by the 3D-finite element method (FEM) and experimental results for several given scenarios. FEM and experimental verifications of this model, make the model suitable for any desirable design in any pulsed power system. Finally, the EMI noise level of the system after optimization is shown and compared to the IEC61800-3 standard.