In this study, the effect of using a blended biodiesel fuel containing 10% rapeseed methyl ester (RME) on the composition and quantity of the chemicals emitted by a modern diesel engine was investigated. The diesel engine that was utilized fulfilled Japan’s Post New Long Term emission standards and was equipped with an after-treatment system comprising a diesel oxidation catalyst and a catalyzed diesel particulate filter (c-DPF). Using the Japanese JE05 transient cycle as the testing cycle, the exhaust gas was sampled for three different states: when the after-treatment system was not deployed, termed “engine-out” (due to the sampling location); when the after-treatment system was deployed, termed “tailpipe-out” (likewise due the sampling location); and when the after-treatment system was deployed and the c-DPF was regenerating, termed “regen”. Evidence from this study indicated that the use of 10% RME biodiesel had no significant impact on the emissions of CO, CO2, the total hydrocarbons, and NOx, which are regulated, regardless of the sampling state. However, the emissions of elemental carbon, organic carbon, and polycyclic aromatic hydrocarbons (PAHs), which are unregulated, showed some effects. During engine-out and tailpipe-out, emissions of the elemental carbon species EC2 were slightly lower when using the biodiesel blend than the petroleum diesel (D) fuel; however, an increase in the organic carbon species OC1 and OC2 and in some PAHs was observed during regen because of the sizable consumption of the biodiesel blend compared to D fuel. These results confirm that 10% RME biodiesel is a promising alternative to fossil fuels for diesel engines, but it is important to grasp the behavior of individual components and carefully investigate the effects of increased mixing ratios.