The present study aimed to investigate the antibacterial and antibiofilm effects of selenium nanoparticles (SeNPs) synthesized by two different methods against Staphylococcus aureus forming biofilm in vivo and in vitro, with a focus on the toxicological and behavioral changes of various SeNPs concentrations in rats. SeNPs were prepared by green and chemical methods and characterized by X-ray diffraction (XRD), Transimission electron microscope TEM. Their antibacterial efficacy was evaluated by agar well diffusion test, also minimal inhibitory concentration (MIC) and the minimal bactericidal concentration (MBC) values were detected. Experimental design sixty female lactating rats were divided into 6 groups: G1 control negative, G2 control positive, G3-G6 infected animals received SeNPs with different concentrations. A bacteriological and histopathological examination of the mammary gland was carried out, an antioxidants assay was evaluated and finally a toxicological study was done. Green synthesized SeNPs showed antibacterial effects at different concentrations (600 μg/mL to 10μg/mL) with MIC and MBC values of 10μg/mL and 25μg/mL. Time kill kinetics showed that SeNPs inhibited the growth of S. aureus completely after 4 hours. The treated group showed pronounced improvement in the main lactiferous duct with normal histological structure compared with the infected group without treatment; by increasing dose the main lactiferous duct structure and acini became nearly identical to the control negative group. Bacteriological examination showed a complete absence of bacterial colonies in all tested concentrations in female rats. The highest doses of SeNPs showed mild cytoplasmic vacuolization of some hepatocytes with activation of kupffer cells with normal hepatocytes structure compared to the control group, a decrease in catalase (CAT) and total antioxidant capacity (TAC) in most examined doses compared to the control group, and an increase in superoxide dismutase (SOD) level in all treated animal. SeNP supplementation could be a safe and helpful treatment for Staphylococcus aureus infection. It prevents biofilms formation both in vitro and in vivo, and it had no notable toxicological or behavioral effects on rats.