Abstract A simple continuous process was designed for the transesterification of Jatropha curcas ( J. curcas) oil to alkyl esters using microwave-assisted method. The product with purity above 96.5% of alkyl ester is called the biodiesel fuel. Using response surface methodology, a series of experiments with three reaction factors at three levels were carried out to investigate the transesterification reaction in a microwave and conversion of alkyl ester from J. curcas oil with NaOH as the catalyst. The results showed that the ratio of methanol to oil, amount of catalyst and flow rate have significant effects on the transesterification and conversion of alkyl ester. Based on the response surface methodology using the selected operating conditions, the optimal ratio of methanol to oil, amount of catalyst and flow rate of transesterification process were 10.74, 1.26 wt% and 1.62 mL/min, respectively. The largest predicted and experimental conversions of alkyl esters (biodiesel) under the optimal conditions are 99.63% and 99.36%, respectively. Our findings confirmed the successful development of a two-step process for the transesterification reaction of Jatropha oil by microwave-assisted heating, which is effective and time-saving for alkyl ester production.