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Abstract Background Staphylococcus aureus (S. aureus) is a common cause of bacteremia, which leads to significant morbidity and mortality. We investigated the relationship between time to positivity (TTP) and clinical outcomes in children with S.aureus bacteremia in the China. Methods A retrospective study of Staphylococcus aureus bacteremia inpatient was performed in Children’s Hospital of Chongqing Medical University in China between 29 January 2014 and 29 August 2017. TTP and clinical parameters were determined and analyzed. The receiver operating characteristic (ROC) curves were plotted for optimal cut-off selection, multivariate logistic regression tests were performed to evaluate the association between TTP and clinical outcomes. Results Overall, 84 cases were enrolled. We stated that in-hospital mortality is significantly higher in the early TTP (≤17 h) than in the late TTP (> 17 h) group (57.14% vs 7.14%, P = 0.000). Septic shock occurred in 57.14% of patients with early TTP and in 18.57% of patients with late TTP (P = 0.002). Detailed multivariate and statistical analysis revealed that early TTP, need for vasoactive agent were independent risk factors of in-hospital mortality; early TTP, need for vasoactive agent and APACHE II score ≥ 15 were independent risk factors of septic shock incidence in S. aureus bacteremia children. Conclusions Overall, TTP of ≤17 h appeared to correlate with the worse outcomes for S. aureus bacteremia children. These results have important implications in the assessments and management of pediatric S. aureus bacteremia in a clinical setting. Trial registration Retrospectively registered.