This study evaluates the thermal comfort and airflow performance of two HVAC configurations in a university lecture room to optimize indoor environmental quality and enhance learning conditions. Conducted in Classroom 1303 at October 6 University, Egypt, the research utilized computational fluid dynamics (CFD) simulations with ANSYS® fleunt to analyze thermal and airflow distribution under two setups. Case 1 featured a free-standing air conditioner with a single inlet and outlet, while Case 2 employed a concealed ceiling-mounted system with two inlets and outlets. The results revealed significant differences between the systems. Case 1 showed uneven cooling, with a temperature gradient of 6–8°C between the front and rear sections, inconsistent airflow velocities of 0.5–0.7 m/s near the windows, and poor air mixing. Relative humidity ranged between 32–42%, reflecting further inconsistencies. In contrast, Case 2 achieved a uniform temperature gradient of 2–3°C, balanced airflow velocities of 0.3–0.5 m/s, and stable relative humidity between 38–42%. Thermal comfort analysis using Predicted Mean Vote (PMV) and Predicted Percentage of Dissatisfied (PPD) indices highlighted Case 2's superior performance, with PPD values consistently below 10%, while Case 1 showed discomfort levels exceeding 25% in localized areas. These findings underscore the concealed ceiling-mounted system's ability to deliver consistent thermal comfort, better airflow distribution, and stable environmental conditions compared to the free-standing air conditioner. This research offers valuable insights for architects and engineers in designing HVAC systems that enhance indoor environmental quality in educational spaces, with future studies recommended to focus on energy efficiency and experimental validation for further optimization.