Due to the rising price of crude oil, biofuel is being considered as a global alternative for fossil fuels to reduce the emission of greenhouse gases. Diesel blended with bio fuel is currently being widely adopted in many countries. The Taiwanese government has been enforcing the adoption of B2 since 2010. However, there have remained consistent concerns about engine durability related to the use of biofuel, especially regarding after-treatment systems. A selective catalytic reduction system (SCR) has been utilized recently to reduce NOX emission in order to meet the Euro IV and V emission standards. To evaluate the impact of biodiesel on the durability of engines equipped with the SCR system, a long-term testing program was organized for the purposes of this study. The results can be used as a reference for the development of marketing promotion strategies as well as government policies in Taiwan. B8 diesel fuel (8 vol% biodiesel) was employed in a commercial heavy duty common-rail fuel injection engine for testing purposes to determine its influence on the durability of engine components and the SCR system. After a 1000-hour full load test operation, the key components of the engines, including the injector, piston ring, and catalyst were analyzed and characterized through a series of inspections to identify the degree of decay and wear behavior. In addition, the engine performance was evaluated with the SAE J1995 test procedure, and the emissions were measured using the ETC test procedure at each maintenance stage and after the durability test to determine any variations in performance and emissions. Furthermore, non-regulatory emissions, such as PM2.5, PM diameter distributions, and particle numbers, which have been proved to be critically important in terms of causing cancer from diesel engine emissions, were also evaluated in this study. It was found that the standard deviation of performance and emissions varied less than 3% when the diesel engine was fueled with B8 biodiesel. The results also indicated that the SCR system still maintained conversion efficiency at 70∼95% after the 1000hr durability tests.