The essential trace element selenium (Se) modulates the functions of many regulatory proteins in signal transduction, conferring benefits in inflammatory diseases. Endometritis is a reproductive obstacle disease both in humans and animals. Staphylococcus aureus is the major pathogen that causes endometritis. The present study analyzes the protection and mechanism of Se-methylselenocysteine (MSC) and methylseleninic acid (MSA) on S. aureus-induced endometritis. An atomic fluorescence spectrophotometry study showed that the uterine Se content increased with the addition of MSC and MSA. Histopathology observation and TUNEL detection showed that Se supplementation displayed a greater defense against uterine inflammatory damage. The quantitative PCR (qPCR) and ELISA analyses showed that the expressions of tumor necrosis factor alpha (TNF-α) and interleukin-6 (IL-6) increased with S. aureus infection and decreased with the addition of MSC and MSA. The Toll-like receptor 2 (TLR2) expression showed the same status as the inflammatory cytokines. The Western blot results showed that the increased phosphorylation of IκBα and NF-κB p65 was also reduced by the addition of MSC and MSA. The qPCR and Western blot results also showed that the transcription expressions and the protein dissociation of caspase-9, caspase-3, caspase-7, caspase-6, and poly(ADP-ribose) polymerase (PARP), which were increased by S. aureus infection, were inhibited by Se supplementation. All of the results displayed that the protection conferred by MSC was stronger than MSA. The present study indicated the Se supplementation might be a potential prevention and control measure for S. aureus-induced endometritis.