Staphylococcus aureus is a common human pathogenic bacteria that can cause serious infections, including lethal staphylococcal pneumonia. The development of antimicrobial resistance has limited treatment options for this pathogen; consequently, novel antibiotics and strategies are urgently desired to combat these infections. In recent years, virulence factors secreted by pathogenic microorganisms have been developed as targets for drug discovery. Alpha-hemolysin, a pore-forming cytotoxin that is secreted by most S. aureus strains, is essential for the pathogenesis of S. aureus pneumonia. In this study, we report that apigenin, a compound extracted from parsley that has no antimicrobial activity vs. S. aureus in vitro, can remarkably decrease the production of α-hemolysin at low concentrations. When added to the A549 cells and S. aureus co-culture system, apigenin protected A549 cells from α-hemolysin-mediated injury. Furthermore, in vivo tests indicated that apigenin alleviated injury of the lung tissue and decreased cytokine levels in the bronchoalveolar lavage fluid in the mouse model of S. aureus pneumonia.