Esterification is required to reduce the high free fatty acid (FFA) content of crude Jatropha oil to below 3% prior to transesterification. In this study, raw decorticated Jatropha seeds were employed as the feedstock in in situ reactive extraction assisted by ultrasound in the presence of sulfuric acid (H2SO4) as a catalyst. Extraction efficiency, esterification efficiency, and fatty acid methyl ester (FAME) yield were optimized as a function of ultrasonic pulse mode, amplitude, and H2SO4 amount. The optimum extraction efficiency of 83.96%, esterification efficiency of 71.10%, and FAME yield of 38.58% were achieved at a pulse mode of 5 s on/2 s off, an ultrasonic amplitude of 60%, and an H2SO4 amount of 5 mL in reaction time of 150 min.