The effect of silicon (Si) inputs has been explored in several wheat/leaf pathogen pathosystems; however, studies in head diseases, i.e., Fusarium head blight (FHB) causing yield and quality losses worldwide, are limited. This 2-year field study evaluated the influence of root application of silicon (Si) to control FHB. The impact of Si at a concentration of 1.7 mM in reducing FHB damage, i.e., disease incidence (DI, Type I resistance), disease severity (DS, Type II) as well as Fusarium-damaged kernels (FDK, Type III), was compared on six bread and durum wheat cultivars contrasting in disease resistance inoculated with four Fusarium species. Root application of Si enhanced all the components of host resistance evaluated in this study; 1.7 mM Si resulted in significantly lower DI, DS and FDK compared with non-Si-treated plants, showing the beneficial role played by this element in decreasing head blight disease symptoms under a broader range of environmental conditions. More importantly, Si augmented inherent host resistance of susceptible to moderately susceptible cultivars measured by DI and DS to the same level of resistance exhibited by a moderately resistant wheat cultivar without Si. On the other hand, Si led to a quasi-similar reduction of FDK regardless of the wheat cultivar. The findings of this report show for the first time that multiple Si root applications supplied continuously into wheat plants improved the effect of genetic resistance in managing FHB. Furthermore, results indicate that Si fertilization is effective as part of an integrated management of wheat head diseases.