High-voltage (HV) pulsed power generators are very important in plasma generation in corona discharge reactors. With the advent of new fast switches technologies such as silicon carbide (SiC) and gallium nitride (GaN), electromagnetic interference (EMI) noise in such systems are very challenging. In this article, electromagnetic compatibility (EMC) modeling and conducted EMI analysis for a pulse generator including an ac-dc-dc power supply are developed. Moreover, the common mode (CM) EMI noise propagation through the system is discussed and the noise sources and effect of each component on the noise flowing are analyzed. The ac-dc-dc power supply role is also investigated and since there is an isolation stage in the system, the effect of high-frequency (HF) transformers that provide a flowing path for noise is also studied. In addition, the CM impedance of different parts of the system as well as the noise voltage are discussed by regarding different values for parasitic parameters of the system. As the system noise level could not meet IEC61800-3 standard, EMI attenuation techniques were applied to the system. By using balance technique and adding filtering inductor as a decoupling inductance, the EMI noise is reduced. Furthermore, an EMI filter optimized and designed for the power supply system that could reduce the EMI noise level. However, by using some EMI reduction techniques that are explained in this article, the size of the required EMI filter is reduced. In this article, EMC modeling, conducted EMI analysis, and EMI reduction techniques led to higher performance and efficiency and lower size of EMI filter that reduced the overall size of the system.