The COVID-19 pandemic has refocused attention to the significance of indoor air quality and how air moves during the circulation process. Contaminants, especially aerosols (≤ 5 µm), remain airborne for prolonged periods and travel long distances increasing the risk of infection to occupants. This study investigated the movement of air and respiratory particles in a clinical setting and an isolation system using computational fluid dynamics. The ventilation system distributes a combination of outdoor and indoor air to reduce energy consumption. The recirculated air carries contaminants smaller than 1 µm, which are distributed to other spaces in the building, increasing the risk of infection to other occupants. Therefore, the efficacy of an airsterilization unit that integrates with a building air handling system was examined. It was observed that a larger percentage of aerosols were exhausted compared to droplets, as larger particles deposit on surfaces under the influence of gravity. Using the air sterilization unit reduced the pathogen concentration in the clinical setting by 25%. The air sterilization system had a significant impact when used in an isolation system with a negative pressure and a positive pressure room. Contaminants from the negative pressure room were distributed to the positive pressure room with the conventional ventilation system. However, sterilizing the recirculated air ensured complete safety of the patient (or other occupants) in the positive pressure room. The findings of these studies can be generalized to any scenario where a centralized ventilation system is employed for thermal comfort and air quality control.