It is important to use vancomycin in a proper manner to ensure optimal drug exposure. Despite extensive use of vancomycin in children, studies on its optimal trough concentration (Ctrough) in the pediatric population remained rare. This retrospective study included children < 18 years old with culture-confirmed methicillin-resistant Staphylococcus aureus (MRSA) bacteremia who were hospitalized in our institute from January 2010 to April 2014. Clinical characteristics, initial vancomycin dose, Ctrough and clinical/microbiological outcomes were retrospectively collected from medical records. Forty-six MRSA bacteremia cases occurring to the patients with a mean age of 22.0 ± 46.9 months were included and all of them were healthcare-associated. Severe diseases requiring intensive care unit (ICU) stay, mechanical ventilation and/or resulting in death were observed in 57.8% (26/45); all-cause 30-day fatality was 11.1% (5/45). An initial Ctrough ≥ 15 μg/mL was achieved in only 4 (8.7%) cases with an average vancomycin dosage of 40.6 ± 7.9 mg/kg/day. Persistent bacteremia at 48 hours after initiation of vancomycin was observed more frequently in children with initial Ctrough < 10 μg/mL than in those with Ctrough ≥ 10 μg/mL (P = 0.032). However, there was no statistically significant difference between the two groups in terms of 30-day mortality and recurrent bacteremia (P = 0.899, and P = 0.754, respectively). Although initial Ctrough may be a useful parameter for minimizing early microbiological failure, it does not predict 30-day fatality or recurrence in pediatric MRSA bacteremia. Further prospective data on vancomycin dosing are needed to find the optimal drug exposure and clarify its impact on clinical outcomes in pediatric populations.