This study describes polychlorinated dibenzo-p-dioxin and dibenzofuran (PCDD/F) behavior during the co-incineration of elutriated mixed incinerator ashes with laboratory waste. The input and output materials during elutriation and incineration processes were sampled and analyzed using a high-resolution gas chromatography/high-resolution mass spectrometry assay. The elutriation process mainly washed out soluble salts and thus resulted in an increase in the level of PCDD/F in the mixed incinerator ashes. After co-incineration with laboratory waste, the PCDD/F concentration of the flue gas met the regulated standard in Taiwan, and the PCDD/F mainly existed as a particulate phase. However, the PCDD/F levels in fly ashes that included elutriated ash in the incinerator were higher than those of fly ashes without it. The co-incineration output-mass/input-mass ratio of elutriated ash with laboratory waste was 0.34. According to the X-ray diffraction analysis results and scanning electron microscopy images, the main crystalline phase of the fly ashes was NaCl. The NaCl came from the reaction of HCl in the flue gas and the NaOH injected in the quenching tower after treatment in the co-incineration system.