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Biodiesel is a nontoxic, biodegradable and renewable fuel with a potential to reduce engine exhaust emissions. Biodiesel used for the current work is jatropha methyl ester (JME). Earlier research, when biodiesel used in neat form, showed deterioration of performance when compared with diesel. The scope of current work is to match the existing diesel performance in all aspects, when the vehicle is fuelled by neat biodiesel (Jatropha). Matching diesel performance with biodiesel was done by remapping electronic control module. This results in power increase, but the vehicle emissions and noise level tends to increase. So tradeoff between performance and emission is achieved by optimizing the engine parameters. Comparative performance was taken with normal diesel and biodiesel in neat form. Different engine characteristics like torque, power, thermal efficiency, exhaust temperature and noise along with emission such as HC, CO, NOx, and Smoke were studied.