The emissions of persistent organic pollutants (POPs) from diesel engines is becoming more important due to their proximity to human beings compared to stationary sources whose emission have been well controlled over the years. The selective catalytic reduction (SCR) have been adopted in the heavy-duty diesel engine (HDDE) to reduce the nitrogen oxide (NOx). SCR has also been reported to reduce the polycyclic aromatic hydrocarbons (PAHs), polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), and polychlorinated biphenyls (PCBs). However, the memory effect and reformation of persistent organic pollutants (POPs) during SCR operation are not well understood. This study investigated the effect of Copper-zeolite SCR (CuZ SCR) on PCDD/F, PCB, polybrominated dibenzo-p-dioxin and dibenzofuran (PBDD/F), and polybrominated biphenyl (PBB) emissions from a HDDE at 50% and 75% engine load. Notably, PCDD/F and PCB toxicity emissions increased by 78.4% and 201%, respectively. The dominant PCDD/F congeners were OCDD, OCDF, 1,2,3,4,6,7,8-HpCDD, and 1,2,3,4,6,7,8-HpCDF and PCB-105, PCB-118 and PCB-77 for PCBs. More PCDFs were formed compared to PCDDs and lower chlorinated congeners increased more than the higher chlorinated ones. There was also an increase of PBDD/F concentrations from undetectable levels (ND) to 0.247 pg TEQ Nm–3 (4.00 pg TEQ L–1) after the SCR. However, only 1,2,3,4,6,7,8-HpBDF and OBDF contributed to the concentrations. PBBs was the only compound measured that reduced after the SCR. The only congener detected before and after the SCR was PBB 15. Consequently, the CuZ SCR could be a source of POPs under mid and high engine loads in this study. Further detail research is required to focus on the formation of POPs on the catalyst surfaces and structures.