PBDES are used as the flame retardants and have adverse effects on human health. Electric arc furnaces (EAF) are one of major emission source of PBDEs. The PBDE contents in the fly ashes of an EAF (29.3 ng/g) examined in this study were one to three orders higher than those in environmental soils. EAF fly ash treatment plants are established to resolve the disposal of this material, and also to recover the remaining iron or zinc from it. However, very little is known about the fate of PBDEs in EAF fly ash treatment plants. The EAF fly ash treatment plant investigated in this work can be divided into three sub-systems, including a pelletizer, reducing furnace and submerged arc furnace (SAF). The fly ash generated from the pelletizer process exhibited the highest PBDE content (7.69 ng/g), and contributed about 91% of the total PBDE inputs (4.40 g/day). The total PBDE concentrations in the stack flue gases of the pelletizer, reducing furnace and SAF were 24.5, 2.88 and 4.71 ng/Nm3, respectively. The high PBDE concentrations of the pelletizer resulted from not only the thermal desorption of lighter brominated congeners, but also fugitive particles of EAF fly ashes. Together, the three stacks accounted for 40.8% of the total PBDE outputs, revealing that the air pollution control devices deployed in the current study were not very effective with regard to removing PBDEs from the flue gas. The PBDE output/input ratio of the EAF fly ash treatment plant was 0.0378, and thus most PBDEs introduced into the system were decomposed. The EAF fly ash treatment plant examined in this work is thus a reliable facility with regard to the disposal of this material.