Biofuels have been widely used in conventional Diesel engines to replace, partially or totally, by fossil diesel. However, the use of an innovative fuel should be evaluated and an important feature to be considered is the ignition delay of the combustion process. Ignition delay can be correlated with activation energy (Ea) and greatly affects the performance of the engine, including pollutant emissions. This study presents the determination of activation energy of three pure fuels -farnesane, biodiesel and fossil fuel -and their blends. In addition, the correlation between Ea and NOx and CO emissions were established. Gases emissions were generated in the OM 926 LA CONAMA p7/EURO 5 diesel engine according to the European Stationary Cicle (ESC). Activation energies were determined by means of thermogravimetric experiments and the mathematic model free-kinetics. Our results indicate that when biodiesel is added to the blend with fossil Diesel, both activation energy values and NOx emission increase, but no direct correlation between Ea and CO emissions was observed. A contrary behavior was observed with farnesane in the blend, i.e., its addition in the fossil Diesel decreases both activation energy and NOx and CO emissions.