Muscle atrophy can be induced by high doses or prolonged use of glucocorticoids. Kaempferol (Kae) is a naturally occurring flavonoid with a variety of biological activities and the effect of Kae on dexamethasone (Dex) induced muscle atrophy in animals has not been elucidated. To explore this issue, the present experiments used a computationally assisted drug design scheme combining network pharmacology, molecular docking and in vivo experiments to investigate the mechanism of Kae against muscle atrophy. Network pharmacological analyses revealed 275 potential targets for Kae and 12294 potential targets for muscle atrophy, with a total of 228 cross-targets for Kae and muscle atrophy. GO and KEGG analyses were performed based on the protein-protein interaction (PPI) network of muscle atrophy and Kae component targets. The GO results showed that the biological processes were mainly related to the metabolic process of reactive oxygen species, and the response to oxidative stress; the cellular components were mainly focused on membrane microdomains, and membrane regions; the molecular functions mainly worked on phosphatase binding; and the KEGG pathway enrichment analyses identified the pathways of interaction between Kae and muscle atrophy. Finally, as verified by in vivo experiments, Kae may reduce the onset of muscle atrophy by activating the PI3K/AKT/mTOR/signalling pathway, inhibiting Foxo1/Foxo3 activity, and inhibiting downstream production of the ubiquitination 3 ligases Atrogin1 and MuRF1; Kae also promotes the expression of NRF2/HO-1/KEAP1 signalling pathway, enhances muscle antioxidant capacity, inhibits the release of COX-2 and TNF-α inflammatory factors, and reduces the damage caused by oxidative stress and inflammatory factors to muscles. Therefore, there may be a synergistic effect of PI3K/AKT/mTOR and NRF2/HO-1/KEAP1 in Kae working together to prevent muscle atrophy. The binding energy and stability of Kae to potential targets were examined by molecular docking and molecular dynamics simulations, implying that Kae could be used for the prevention and treatment of muscle atrophy in patients.