ABSTRACT Background: Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is spreading worldwide, but little is known about the epidemiology of this pathogen in Brazil. Objective: To evaluate clinical and microbiological features of children with S. aureus infections admitted to a university hospital. Methods: This was a cross-sectional study evaluating the potential risk factors for CA-MRSA, and a retrospective cohort evaluating in-hospital clinical outcomes. To include patients with both community and hospital-associated infections, we screened the results of the microbiological laboratory tests from January 1, 2012, to December 31, 2016. According to the phenotype, we classified the isolates in Methicillin-Susceptible S. aureus (MSSA), Hospital-Associated Methicillin-Resistant S. aureus (HA-MRSA), and CA-MRSA. Clinical data were collected from the patients’ medical records. Results: We identified 279 cases of S. aureus infections (MSSA = 163, CA-MRSA = 69, HA-MRSA = 41). Overall, the incidence density of CA-MRSA and MSSA infections increased while the HA-MRSA incidence density decreased over the study period. CA-MRSA infected patients were more likely to present with skin and soft tissue infections (OR: 2.83, 95%CI: 1.54–5.33, p < 0.001) and osteomyelitis (OR: 4.76; 95%CI: 1.16–22.71, p = 0.014) when compared to MSSA and HA-MRSA infections. Unadjusted case fatality rates were similar between MSSA-infected patients (3.14%, 5/159) and CA-MRSA infected patients (3.80%, 3/79, p = 0.792), while HA-MRSA infected patients were more likely to die in the hospital (12.20%, 5/41, p = 0.013). Conclusions: CA-MRSA is an emergent pediatric pathogen in Brazil. Our results highlight the relevance of choosing an appropriate initial antimicrobial drug for treating children with severe S. aureus infections.