To understand the fate of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in a fly ash treatment plant that used the Waelz rotary kiln process (hereafter the Waelz process), the samples of input and output media were collected and analyzed. The most important PCDD/F source in input mass was electric arc furnace (EAF) fly ash, which had a mean PCDD/F content of 18.51 ng/g and contributed more than 99% of PCDD/F input mass, whereas the PCDD/F input mass fractions contributed by the coke, sand, and ambient air were only 0.04%, 0.02%, and 0.000002%, respectively. For the PCDD/F output mass in the Waelz process, the major total PCDD/F contents of 43.73 and 10.78 ng/g were in bag-filter and cyclone ashes, which accounted for approximately 69% and 17%, respectively, whereas those of stack flue gas and slag were 14% and 0.423%, respectively. The Waelz process has a dechlorination mechanism for higher chlorinated congeners, but it is difficult to decompose the aromatic rings of PCDD/Fs. Therefore, this resulted in the accumulation of lower chlorinated congeners. The output/input ratio of total PCDD/F mass and total PCDD/F international toxicity equivalence (I-TEQ) was 0.62 and 1.19, respectively. Thus, the Waelz process for the depletion effect of total PCDD/F mass was positive but minor, whereas the effect for total PCDD/F I-TEQ was adverse overall.