The synthesis of fatty acid ethyl esters (FAEEs) by a two-step in situ (reactive) esterification/transesterification from Jatropha curcas L. (JCL) seeds using microwave system has been investigated. Free fatty acid was reduced from 14% to less than 1% in the first step using H2SO4 as acid catalyst after 35 min of microwave irradiation heating. The organic phase in the first step was subjected to a second reaction by adding 5 N KOH in ethanol as the basic catalyst. Response surface methodology (RSM) based on central composite design (CCD) was utilized to design the experiments and analyze the influence of process variables (particles seed size, time of irradiation, agitation speed and catalyst loading) on conversion of triglycerides (TGs) in the second step. The highest triglycerides conversion to fatty acid ethyl esters (FAEEs) was 97.29% at the optimum conditions:<0.5mm seed size, 12.21 min irradiation time, 8.15 ml KOH catalyst loading and 331.52 rpm agitation speed in the 110 W microwave power system.