Sunflower (Helianthus annuus L.) is one of the three most productive oilseed crops worldwide. Soilborne diseases limit yields and are challenging to manage. The fungi Verticillium dahliae, Sclerotinia sclerotiorum and Macrophomina phaseolina can survive in the soil for many years and spread. Following the ban on fumigants, biofumigation, which consists of growing, chopping and incorporating a Brassicaceae cover crop to allow biocidal compounds production in the soil, may be an alternative. Biocidal effects of the hydrolysis of glucosinolate into active compounds, such as isothiocyanates, have been shown in laboratory studies, but the effectiveness of biofumigation varies more in the field. The present study reviews the main factors that determine effective biofumigation to protect sunflower. Since the toxicity of isothiocyanates to pathogens varies widely among the latter, we reviewed studies that assessed the suppressive effect of products of glucosinolate hydrolysis on V. dahliae, S. sclerotiorum and M. phaseolina. Farmers can use many mechanisms to increase isothiocyanate production, which may protect sunflower crop effectively. Increasing biomass production and chopping the cover crop during mild temperatures and before rainy periods could increase biofumigation effectiveness. Further field experiments are needed to confirm the potential of biofumigation to control soilborne diseases of sunflower and assess potential disservices to beneficial soil communities, given their potential key role in the control of soilborne pathogens.