Acyltransferase (AT) catalyzes the transfer of an acyl moiety from acyl-coenzyme A (acyl-CoA) to an acceptor. ATs play important roles in the maintenance of homeostasis in the human body and have been linked to various diseases; therefore, several ATs have been proposed as potential targets for the treatment or prevention of such diseases. The AT family includes acyl-CoA:cholesterol AT (ACAT), diacylglycerol AT, and monoacylglycerol AT for the metabolism of lipids. Furthermore, recent molecular biological studies revealed the existence of their isozymes with distinct functions in the body. ACAT plays a critical role in the formation of cholesteryl esters from cholesterol and fatty acids, and is a potential target for treating hypercholesterolemia. During an experiment designed to discover biologically active compounds from herbal medicines, we isolated two known guaianolide sesquiterpene lactones from Chrysanthemum boreale Makino (Compositae). The lactones were characterized from their spectroscopic data (NMR, IR, MASS). These compounds were subjected to ACAT inhibition assay. Here, we report the isolation and structural elucidation of the compounds 8-o-acetyl-2-methoxy-10-hydroxy-3,11(13)-guaiadiene-12,6-olide and 8-acetyl-3,10-hydroxy-4(15),11(13)-guaiadiene-12,6-olide. In the ACAT inhibition assay, compound 1 showed strong inhibitory activity, with an IC50 value 45 μg/mL, whereas compound 2 did not exhibit significant inhibitory activity with an over 100 μg/mL.