Clinical infections caused by Staphylococcus aureus (S. aureus) will likely remain common and serious. Not only there has been an increase in antimicrobial resistance, but also the spectrum of clinical disease continues to increase. Our aim in this research is to determine the prevalence as well as to identify and characterize the pattern of resistance of S. aureus isolates recovered from pediatrics with otitis media admitted to tertiary hospitals in Alexandria, Egypt. Out of 180 clinical samples, 193 different bacterial isolates were recovered. Along with Pseudomonas aeruginosa, S. aureus was the predominant (18.6%) pathogen isolated. Antibiotic susceptibility testing among S. aureus isolates revealed that up to 27 (75%) out of the tested isolates exhibited high (> 0.2) MAR index values. Methicillin-resistant S. aureus (MRSA) isolates were determined using the minimal inhibitory concentration (MIC) of cefoxitin. The incidence of MRSA among S. aureus isolates was 44.4%. On the other hand, none of the tested isolates was linezolid resistant. The presence of methicillin resistance genes (mecA and femA) and aminoglycoside resistance genes (aac (6′)Ie/aph(2′′)Ia, aph(3′)-IIIa and ant(4′)-Ia) were detected using Polymerase Chain Reaction (PCR) technique. The incidence of aac (6′)Ie/aph(2′′)Ia, aph(3′)-IIIa and ant (4′)-Ia was 38.9%, 36.1% and 30.6%, respectively. Besides, the incidence of cap8, cap5 and lukS/F-PV virulence genes was 33.3%, 25% and 11.1%, respectively. Accordingly, we recommend the necessity of continuous surveillance and control of antimicrobial resistance and virulence level in S. aureus as one of the major pathogens of pediatric otitis media in Alexandria, Egypt.