The platelet-activating factor receptor (PAFR) has been a therapeutic target for platelet- activating factor (PAF)-mediated diseases. The pathophysiological condition is triggered by the interaction of PAF agonist. The discovery of PAF antagonists from natural flavonoids could be promising candidates for treating PAF-mediated diseases. Flavonoids that exist in most edible plants possess good health benefits to the human body. The study aimed to investigate the ability of three flavonoids (apigenin, galangin and fisetin) for molecular docking and dynamic simulations into PAFR protein. The PAFR-flavonoid complex binding affinities and interactions were assessed through molecular docking and dynamic simulations. Results found that all flavonoids significantly have a good binding affinity, ranging from - 9.1 to - 8.9 kcalmol-1. The stability of these flavonoids was also achieved in a 30 ns simulation. Four critical residues were detected in all PAFR-flavonoids complexes (Phe97, Phe98, Thr101 and Leu279) from the analysis of MMGBSA binding free energy. Interactions of van der Waals and electrostatic were seen by individual key residues of PAFR for the free energy contribution of ligands binding. All flavonoids showed promising anti-PAF candidate to be developed in the future.