The purpose of heating, ventilation, and air conditioning (HVAC) systems are to create optimum thermal comfort and appropriate indoor air quality (IAQ) for occupants. Air ventilation systems can significantly affect the health risk in indoor environments, especially those by contaminated aerosols. Therefore, the main goal of the study is to analyze the indoor airflow patterns in the heating, ventilation, and air conditioning (HVAC) systems and the impact of outlets/windows. The other goal of this study is to simulate the trajectory of the aerosols from a human sneeze, investigate the impact of opening windows on the number of air changes per hour (ACH) and exhibit the role of dead zones with poor ventilation. The final goal is to show the application of computational fluid dynamics (CFD) simulation in improving the HVAC design, such as outlet locations or airflow rate, in addition to the placement of occupants. In this regard, an extensive literature review has been combined with the CFD method to analyze the indoor airflow patterns, ACH, and the role of windows. The airflow pattern analysis shows the critical impact of inflow/outflow and windows. The results show that the CFD model simulation could exhibit optimal placement and safer locations for the occupants to decrease the health risk. The results of the discrete phase simulation determined that the actual ACH could be different from the theoretical ACH as the short circuit and dead zones affect the ACH.