In 2016, a cross-sectional study was conducted in order to evaluate the prevalence of nasal carriage of methicillin-resistant Staphylococcus aureus and its antibiotic susceptibility pattern among children attending two pediatric public hospitals in capital town of Madagascar. Results show that the prevalence average of nasal carriage of MRSA was 13.49 %. Age between 5 to 15 years old and history of hospitalization were found to represent a risk factor of MRSA nasal carriage (OR 6.632, 95% CI 1.821 to 24.15 p = 0.001; OR 11.46, 95% CI 3.448 to 38.11; P = 0.002, respectively). Among MRSA nasal isolates, a high rate of multidrug resistance and particularly a resistance to Trimethoprim-sulfamethoxazole (81.25%) and Amoxicillin+clavulanic acid (70.13%) were observed. These results suggest that MRSA is fully established in Malagasy community which requires urgent strategic policy in order to slow down the spread of these strains.