This study presents a numerical investigation of the annealing process in an industrial-scale continuous container glass annealing furnace. A detailed conjugate thermal model of the furnace is developed where all the heat transfer modes inside the furnace were considered. Special attention was given to the modeling of the radiation heat transfer where the glassware was considered in full-geometrical detail. The model was validated with the furnace temperature data. Next, two case studies were conducted to study the effect of changing the position of the active tubular burners inside the heating zone of the furnace. Results have shown that changing the active burner positions does have a rather weak effect on the air temperature inside the furnace but a more considerable effect on the glassware temperatures. Also, activating the tubular burners away from the furnace inlet and deactivating the burners at the furnace entry results in a more gradual and uniform heating pattern on glassware. This study signifies the importance of active burner positions on the heat transfer in the furnace.