To determine risk factors for complications in children with Staphylococcus aureus (S aureus) bacteremia, including methicillin resistance. Single center, retrospective cohort study of children ≤18 years of age hospitalized with S aureus bacteremia. We compared clinical characteristics and outcomes between those with methicillin-sensitive S aureus (MSSA) and methicillin-resistant S aureus (MRSA) bacteremia. Multivariate regression models identified risk factors associated with developing complications and with longer duration of bacteremia. We identified 394 episodes of S aureus bacteremia, 279 (70.8%) with MSSA, and 115 (29.2%) with MRSA. Primary site of infection was catheter-related in 34%, musculoskeletal in 30%, skin/soft tissue in 10.2%, pneumonia in 6.4%, and endovascular in 6.6%. Eight children (2.0%) died within 30 days because of S aureus bacteremia, 15 (3.5%) had recurrence within 30 days, and 38 (9.6%) had complications including septic emboli or a metastatic focus of infection. Methicillin resistance was associated with development of a complication (aOR 3.31; 95% CI 1.60-6.85), and catheter-related infections were less likely to be associated with a complication (aOR 0.40; 95% CI 0.15-1.03). In a Poisson regression analysis on duration of bacteremia, methicillin resistance, musculoskeletal infection, endovascular infection, black race, and delayed intervention for source control were significantly associated with longer duration of bacteremia. In this cohort of children with S aureus bacteremia, MRSA infections ere associated with longer duration of bacteremia and a higher likelihood of complications.