Septic arthritis is the most aggressive joint disease associated with high morbidity and mortality. The interplay of the host immune system with the invading pathogens impacts the pathophysiology of septic arthritis. Early antibiotic treatment is crucial for a better prognosis to save the patients from severe bone damage and later joint dysfunction. To date, there are no specific predictive biomarkers for septic arthritis. Transcriptome sequencing analysis identifiedS100a8/a9genes to be highly expressed in septic arthritis compared to non-septic arthritis at the early course of infection in anStaphylococcus aureusseptic arthritis mouse model. Importantly, downregulation ofS100a8/a9mRNA expression at the early course of infection was noticed in mice infected with theS. aureusSortase A/B mutant strain totally lacking arthritogenic capacity compared with the mice infected with parentalS. aureusarthritogenic strain. The mice infected intra-articularly with theS. aureusarthritogenic strain significantly increasedS100a8/a9protein expression levels in joints over time. Intriguingly, the synthetic bacterial lipopeptide Pam2CSK4 was more potent than Pam3CSK4 in inducingS100a8/a9release upon intra-articular injection of these lipopeptides into the mouse knee joints. Such an effect was dependent on the presence of monocytes/macrophages. In conclusion,S100a8/a9gene expression may serve as a potential biomarker to predict septic arthritis, enabling the development of more effective treatment strategies.