Menthol is a naturally occurring cyclic terpene alcohol of plant origin from the Lamiaceae family. It has three chiral centres, implying eight possible different stereoisomers, which in turn define four pairs of enantiomers. This is the first work that reports on the stereoselective antifungal and antitoxigenic activities of the menthol stereoisomers on Fusarium verticillioides, with the (−)-menthol and (+)-menthol enantiomers found to be the most active inhibitors of fungal growth and sporulation. The results obtained suggest the importance of the presence of these substituents in the equatorial positions of menthol stereoisomers in the antifungal activity. The stereoisomer (−)-menthol, followed by (+)-menthol, were the most active compounds in the inhibition of fumonisin B1 (FB1) biosynthesis. The different antitoxigenic activities of (−)-menthol and (+)-menthol revealed that the molecular requirements to affect the FB1 production were dependent not only on the presence of the substituents in the equatorial positions, but also on their spatial arrangements.