The study includes an investigation on the polychlorinated dibenzo-p-dioxins (PCDD/Fs) mass fluxes of a hazardous waste incinerator in the operation conditions, which occurred shortly after two different start-up periods. The samples were taken from seven possible dioxin output points through the incineration and air pollution control units, which include bottom ash, boiler fly ash, electrostatic precipitator (ESP) fly ash, treated wastewaters and filter cake from the physicochemical treatment of dual wet scrubbers and fly ashes, activated carbon (AC) bed, and stack gas, and they were analyzed for the PCDD/Fs. The results were assessed to determine the emission factors and the mass fluxes of PCDD/Fs for all of the outputs. A review of the congener profiles suggested that start-up conditions, such as the start-up duration and the cleaning process, may have an effect on the concentrations and congener profiles of PCDD/Fs, especially observed in the fly ashes and the stack gas. Considerable concentrations of low chlorinated furans in the ash outflows were attributed to the heterogeneous de novo synthesis of PCDD/Fs on the fly ash surfaces. Congener contributions to the mass flux of each outflow showed that the congeners retained in bottom ash are generally highly chlorinated ones, while the congeners retained by AC bed or released to the atmosphere are predominately low chlorinated ones. The results indicated that a short and clean start-up procedure in terms of a reasonable emission factor in the stack may be needed.