Background: Currently, the role of microRNAs in plant immune responses is being actively studied. Thus, our aim was to research the effect of Stagonospora nodorum (Berk.) NEs SnToxA and SnTox3 on the expression of miRNAs involved in the wheat–S. nodorum interaction and to determine the role of phytohormones in this process. Methods: The expressions of nine conserved microRNAs were studied by quantitative real-time polymerase chain reaction in three different wheat genotypes of bread spring wheat (Triticum aestivum L.) infected with S. nodorum. Phytohormone treatments (trans-zeatin, 2-chloroethylphosphonic acid (etefone is the chemical precursor of ethylene), and salicylic acid) were applied. The results were compared with disease symptoms, the redox status of plants, and the expression of fungal necrotrophic effector (NE) genes of SnToxA and SnTox3 and genes of SnPf2, SnStuA, alongside SnCon7 transcription factors (TFs). Results: Salicylic acid (SA) and cytokinins (CK) are involved in the development of defense reactions in wheat plants against S. nodorum, by regulating the expression of fungal NEs and TFs genes, inducing an oxidative burst in all three wheat genotypes. Moreover, ethylene enhanced the virulence of the pathogen by increasing the expression of fungal NE and TF genes, thereby resulting in a decrease in the generation of reactive oxygen species in all three cultivars. The nine miRNAs played a role in the development of wheat resistance against S. nodorum. NE SnTox3 mainly suppressed the expression of three miRNAs: miR159, miR393, and miR408, while NE SnToxA suppressed miR166 expression. Conversely, treatment with CK and SA increased the expression of miR159 and miR408; treatment with CK increased the expression of miR393 and miR166. Ethylene inhibited the expression of miR159, miR408, miR393, and miR166. Suppression of miP159 expression by NE SnTox3 was most likely associated with the activation of the ethylene signaling pathway. NEs SnToxA and SnTox3 suppressed the expression of miR408, whose role most likely consisted of inhibiting the catalase activity, via SA and CK regulation. In addition, NE SnToxA hijacked the SA signaling pathway and manipulated it for fungal growth and development. Fungal TFs SnPf2 and SnStuA could be involved in the regulation of these processes indirectly through the regulation of the expression of NE genes. Conclusions: The results of this work show, for the first time, the role of microRNAs in the development of wheat resistance against S. nodorum and the effect of S. nodorum NEs SnToxA and SnTox3 on the activity of plant microRNAs.