In the aluminum production industry, metal furnaces are operated by diffusion flame over the metal surface to maintain the aluminum metal at the set point temperature for alloying and casting. Heat is transferred from the flame and its exhaust gases to the metal surface via radiation and convection. The exhaust gases leaves through the furnace’s chimney carrying a significant amount of waste heat to the atmosphere. Furnace efficiency could be improved by enhancing the heat transfer inside the furnace. In this study, a validated full-scale 3-D CFD model of a natural gas fired aluminum furnace is developed to investigate the effect of flue gas ventilation configurations and burner operating conditions on the heat transfer inside the furnace. Onsite measurements are carried out for the fuel and airflow rates as well as flue gas temperature. Four flue ventilation configurations are considered with eight furnace’s operation modes. The flue-gas’s waste-heat varies from 49–58%, with the highest value occurring at the high-fire operating mode. This indicates a significant room for improvement in the furnace performance. Results suggest that a symmetrical positioning of the exhaust duct favors effective exhaust gas circulation within the furnace and hence, increases hot-gases’ heat-transfer effectiveness inside the furnace. These results provide some guidelines for optimal aluminum reverberatory furnace designs and operation.