Background Natural nutrition and physical training have been defined as non-pharmacochemical complementary and alternative medicines to prevent and treat various pathogenesis. Royal jelly possesses various pharmacological properties and is an effective therapeutic supplement for halting neurodegeneration. Multiple sclerosis is a prevalent neurodegenerative disorder that manifests as a progressive neurological condition. Inflammation, hypoxia, and oxidative stress have been identified as significant hallmarks of multiple sclerosis pathology. Results In the present study, based on artificial intelligence and bioinformatics algorithms, we marked hub genes, molecular signaling pathways, and molecular regulators such as non-coding RNAs involved in multiple sclerosis. Also, microRNAs as regulators can affect gene expression in many processes. Numerous pathomechanisms, including immunodeficiency, hypoxia, oxidative stress, neuroinflammation, and mitochondrial dysfunction, can play a significant role in the MSc pathogenesis that results in demyelination. Furthermore, we computed the binding affinity of bioactive compounds presented in Royal Jelly on macromolecules surfaces. Also, we predicted the alignment score of bioactive compounds over the pharmacophore model of candidate protein as a novel therapeutic approach. Based on the q-RT-PCR analysis, the expression of the Dnajb1/Dnajb1/Foxp1/Tnfsf14 and Hspa4 networks as well as miR-34a-5p and miR155-3p were regulated by the interaction of exercise training and 100 mg/kg Royal Jelly (ET-100RJ). Interestingly, characteristics, motor function, a proinflammatory cytokine, and demyelination were ameliorated by ET-100RJ. Discussion Here, we indicated that interaction between exercise training and 100 mg/kg Royal jelly had a more effect on regulating the microRNA profiles and hub genes in rats with Multiple sclerosis.