The preparation of thioesters through the lipase-catalysed transesterification reaction of thiols with vinyl carboxyl esters is described. The reactions were carried out by Lipase TL IM from Thermomyces lanuginosus as a catalyst and performed under a continuous flow microreactor. We first found that lipase TL IM can be used in the reaction of thioester synthesis with high efficiency. Various reaction parameters were investigated including substrate molar ratio, reaction time, and temperature. Maximum conversion (96%) was obtained under the optimal condition of a substrate molar ratio of 1:2 (4-methylbenzyl mercaptan:vinyl esters) at 50 °C for about 30 min. Compared with other methods, the salient features of this work include mild reaction conditions (50 °C), short reaction times (30 min), high yields, and environment-friendliness.