Biotic stress, which includes infection by pathogenic fungi, causes losses of wheat yield in terms of quantity and quality. Ear Fusarium is caused by strains of F. graminearum and F. culmorum, which can produce mycotoxins—deoxynivalenol (DON) and nivalenol (NIV). One of the wheat’s defense mechanisms against stressors is the activation of biosynthesis pathways of antioxidant compounds, including ferulic acid. The aim of the study was to conduct pilot studies on the basis of which neural models were created that would examine the impact of the variety and weather conditions on the concentration of ferulic acid, and link its content with the concentration of deoxynivalenol and nivalenol. The plant material was 23 winter wheat genotypes with different Fusarium resistance. The field experiment was conducted in 2011–2013 in Poland in three experimental combinations, namely: with full chemical protection; without chemical protection, but infested with natural disease (control); and in the absence of fungicidal protection, with artificial inoculation by genus Fusarium fungi. As a result of the pilot studies, three neural models—FERUANN analytical models (ferulic acid content), DONANN (deoxynivalenol content) and NIVANN (nivalenol content)—were produced. Each model was based on 14 independent features, 12 of which were in the form of quantitative data, and the other two were presented as qualitative data. The structure of the created models was based on an artificial neural network (ANN) of the multilayer perceptron (MLP) with two hidden layers. The sensitivity analysis of the neural network showed the two most important features determining the concentration of ferulic acid, deoxynivalenol, and nivalenol in winter wheat seeds. These are the experiment variant (VAR) and winter wheat variety (VOW).