Abstract Plants produce diverse types of secondary metabolites, including phenolic compounds, which are involved in protection against fungal infections. Sunflower hulls, an under-appreciated by-product of the oil industry, is a natural source of phenolic compounds. The aim of this work was to characterize the composition of natural extracts from sunflower hulls, evaluate their ability to inhibit the growth of phytopathogenic fungi and provide insights on its mechanism of action. We obtained an extract enriched in phenolic compounds (EPC) by hydroalcoholic extraction of sunflower hulls. The analysis by LC-MS/MS showed that the main phenolic compound of EPC was chlorogenic acid. The extract exhibited strong antioxidant activity determined by radical scavenging assay. Through different experimental approaches, we demonstrated that EPC at a concentration of 0.4 mg/mL exerts a fungicidal action against the phytopathogenic fungi Sclerotinia sclerotiorum, Fusarium solani, Fusarium oxysporum, Verticillium dalhiae and Botrytis cinerea. EPC displayed cytotoxic effects mediated by membrane permeabilization and oxidative stress on fungal cells. Our findings contribute to valorize an agro-industrial by-product that is usually discarded, through its potential application as a biofungicide.