Advances in aftertreatment technologies, such as Diesel Particulate Filters (DPF) and Selective Catalytic Reduction (SCR) catalysts, have responded to increasingly stringent PM and NO requirements for diesel engines. Potentially viable SCR materials include copper and iron zeolite, which possess high thermal durabilities and conversion efficiencies. However, concern exists over the metal-catalyzed synthesis of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs), especially since typical SCR operating temperatures overlap with optimal PCDD/F formation from the de novo and precursor mechanisms. Due to the lack of standardized testing methodology for measuring PCDD/F emissions from mobile sources, this study adapted EPA methods 0023A and TO-9A from their original applications of industrial stack and ambient air sampling. The modifications detailed in this paper accommodated the measurement of PCDD/Fs from a dynamometer-controlled engine, addressing considerations such as temperature excursions, concentrated emissions, transient conditions, and engine vibrations. To validate the modified TO-9A approach, measurements were compared to the previously published results of an EPA-certified CVS tunnel for NO, CO₂, and PM emissions and a CRC study for PAHs and aromatics emissions. The modified TO-9A approach was further compared to the modified 0023A approach by performing simultaneous tests over a steady-state cycle using an engine equipped with a copper zeolite SCR system. Although both approaches were capable of detecting ultra-low concentrations of total PCDD/Fs, the modified 0023A approach showed better detectability for the 17 toxic PCDD/F congeners. Furthermore, the modified 0023A approach demonstrated higher precision as determined from statistical analysis of sample-to-sample variation. However, application of the modified 0023A approach to transient conditions would require further development of proportional sampling, without significantly compromising the detectability and precision associated with raw gas analysis.