Pulsed microwave technique was employed for the production of biodiesel from Chlorellasp. via transesterification. Real-time microwave power and temperature profiles were used for the evaluation of efficiency of biodiesel production. The effect of power setting was determined in the range of 100-1000W at the fixed reaction time (10min) and temperature (60 degrees C). In this work, the highest yield of biodiesel per unit energy consumption observed was 0.53% by weight of crude lipid per kilo joule at 250W. From the results in this study, the efficiency of biodiesel production was correlated to the uniform pulse intensity and pulse frequency during the reaction process provided at the power setting of 250W.