Fusarium is a ubiquitous hyalohyphomycete fungus usually isolated from food, which is widespread in different environments (plant, grain, soil) and present at all latitudes. This genus has been widely studied due to its ability to infect, cause tissue destruction and produce mycotoxins on important crops such as corn, wheat and other small grains. Over recent years, much effort has been directed at the search for new antifungal materials from natural sources, and many antimicrobial compounds coming from plants have been identified. Although the essential oils and their components have been recommended as fumigants for preservation of food commodities, little is known about the molecular properties related to the antifungal activity. In the present study, we performed a QSAR study for the inhibition of Fusarium verticillioides growth by ten natural phenolic compounds, which could serve as a guide for the rational design of further inhibitors. The results of the experimental determinations demonstrated that in terms of the antifungal activity of natural phenolic compounds on F. verticillioides, the following order was found: carvacrol > thymol > isoeugenol > eugenol > vanillin > creosol > m-cresol > o-cresol, p-cresol, and guaiacol. Mathematical models based on molecular properties, Lipophilicity, Molar refractivity and Saturated area were found to be the descriptors that best explained the antifungal activity of these compounds. These models could be used in future to predict the activity of new compounds and to guide the search for the synthesis of phenolic compounds with the capacity to alter F. verticillioides growth.