Background: Superantigens of Staphylococcus aureus namely enterotoxin A, exfolia-tive toxin A, and Toxic shock syndrome toxin-1 cause detrimental effects on the cells of the immune system. Methods: In this work, the toxins were downloaded from the Protein DataBank database and en-ergies were minimized using KoBaMIN server. Forty flavonoids compounds were identified by pubchem compound database through extensive literature study and their 3D structures were ob-tained by submitting SMILES to CORINA tool. Based on Lipinski’s rule of five, the molecules were filtered that resulted in 27 compounds. Molecular docking was performed for identifying the binding and interaction sites of flavonoids with the toxins using Autodock 4. Results and Conclusion: The docked complexes were then subjected to molecular dynamics simulation using Gromacs. The analysis revealed the stability of the complexes as indicated by three hydrogen bonds formed during the simulation time period of 20 ns. © 2020 Bentham Science Publishers.