In this study, the 60,000-km durability tests were performed on two diesel engines (EURO IV and EURO II) by using B10 (10% waste cooking oil + 90% diesel) and B8 (8% waste cooking oil + 92% diesel), respectively, to determine the impacts on the emissions of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated dibenzo-p-dioxins and dibenzofurans (PCCD/Fs). The above emissions were measured per 20,000-km testing intervals. The highest total PAH mass concentrations were 38.2 and 25.6 µg Nm–3 before durability test by operating the EURO IV and II engines, respectively, and decreased 51–55% after 60,000-km operation. The dominant congeners of PAH emissions were naphthalene (> 45%), pyrene, and phenanthrene, which belonged to the LM-PAHs. The total PAH BaPeq had different emission trends between the two engines during the durability tests. The highest level was 2.17 µg BaPeq Nm–3 from EURO II engine before the test and reduced 84% after a 60,000-km cycle, when the total-BaPeq emissions of EURO IV tended to increase from 0.0894 to 0.154 µg BaPeq Nm–3 after the same test. The most dominant congener to the toxicity emissions was benzo(a)pyrene (~70%). Additionally, the PCDD/F emissions were tested in EURO IV engine by using B10. The PCDD/F concentrations of mass and toxicity approached the highest levels, 167 ng Nm–3 and 3.69 pg WHO-TEQ Nm–3, after 60,000-km and 20,000-km running cycles, respectively. The main dominant congeners were OCDD (> 50%) for mass, 2,3,7,8-TeCDD (> 35%) and 1,2,3,7,8-PeCDD (> 18%) for toxicity. Consequently, the use of WCO-biodiesel might reduce the PAH mass and toxicity emissions in older engine but had no significant effect in PAH and PCDD/F emissions during the deterioration of a newer engine.