This study examined the effect of using waste cooking oil (WCO) as an alternative of diesel on PBDE emissions during the start-up of an industrial waste incinerator (IWI). The co-combustions were designed with 0, 40, and 60% WCO injection and become D100, W40D60, and W60D40 multi-fuel combustions. The flue gas was sampled during 4 temperature stages of the furnace: Stage A (< 200°C), Stage B (200–450°C), Stage C (580–700°C), and Stage D (> 850°C). The highest PBDE level was found in Stage A and sharply declined in Stage B by using diesel. The reduction of total PBDE was a competitive result between residue releasing and thermal decomposition in Stage B. The WCO were found to slightly increased the PBDE emissions during the Stage C and D, which provided the suitable temperature for PBDE formation (600–800°C). Therefore, the viscosity became an important control factor when the WCO were utilized as an alternative fuel in IWI operation. The accumulated PBDE emissions during the start-up procedure were 1,099, 1,253, and 1,207 µg by using D100, W40D60, and W60D40, respectively. Additionally, the annual PBDE emissions contributed by start-up procedures increased up to 4.60%, 5.47%, and 5.20% by three fuel combinations, respectively, if the IWI restarted once per month, and became a noticeable issue. Therefore, avoiding unnecessary start-ups was an essential criterion for IWI operation. The small increases (< 1%) of PBDE emissions by altering 40% and 60% diesel with WCO provided a useful information for WCO treatment. This new disposal for waste oil also created a good demonstration of Circular Economy. The overall life-cycle analysis was suggested to be investigated in the following research.