Illegal harvesting and recycling of waste cooking oil, also referred to as “gutter oil” in many countries, poses a great food safety threat. Thus, in this study the feasibility of using waste cooking oil as an auxiliary fuel in the furnace of laboratory waste incinerator was evaluated in terms of toxic pollutant emissions. Two fuel blends (W20D80 and W40D60) were blended from varying proportions of diesel fuel (D100), and waste cooking oil (W100) and their physio-chemical characteristics were subsequently determined and compared. Thermogravimetry analysis (TGA) and derivative thermogravimetry (DTG) of D100, W100, W20D80 and W40D60 showed that diesel fuel consist of more volatile short aliphatic hydrocarbons, while the waste cooking oil and its blends had more thermal stable unsaturated long chain molecules. After the de novo synthesis window of 200–400°C, 40% of waste cooking oil and 60% of diesel (W40D60) was injected at around 500–700°C, and reduced the toxicity concentrations of PCDD/Fs and PCBs by an average of 86% and 94%, respectively. This study demonstrated that, by using waste cooking oil as a fuel blend, not only can reduce the possibility of “gutter oil” being put in the food to damage the health of human beings, but also can be recycled as a kind of green fuel to reduce the emissions of persistent organic pollutants (POPs).