With the goal of utilizing Jatropha crude oil (JCO) as a fuel in diesel engines, we have developed a technique for the selective extraction of triglycerides from Jatropha seeds, containing glycerides, free fatty acids, phosphorus, and water, using supercritical CO2 extraction. To evaluate the feasibility of using the extracted JCO as a substitute for diesel fuel in diesel engines, the performance and emission characteristics of a diesel engine fueled by JCO/diesel blends were investigated. We found that it was not possible to completely remove the free fatty acid and moisture content from the JCO using the supercritical extraction method. In addition, no remarkable differences in thermal effciency and specific fuel consumption were observed between JCO and diesel fuel. On the other hand, the amount of CO emissions from JCO was lower than that from the diesel fuel, owing to the complete combustion of CO at high engine loads. Based on the results of the previous study, JCO appears to be a viable substitute for diesel in diesel engines, although the long-term performance of the engine fueled by JCO needs to be further evaluated.