Staphylococcus aureus (S. aureus) is a leading cause of infections in children. The emergence of multidrug-resistant (MDR) strains, especially methicillin-resistant S. aureus (MRSA), presents significant therapeutic challenges. Data on molecular resistance and virulence determinants in pediatric isolates from Egypt remain limited. This retrospective study analysed 120 non-duplicate S. aureus isolates recovered from pediatric patients. Antimicrobial susceptibility testing (AST) was performed using the CLSI disk diffusion method. Conventional PCR detected resistance genes (mecA, blaZ, ermA/B/C, msrA, mphC, tetK, tetM, aminoglycoside-modifying enzyme (AME) genes, and qacA/B) and the Panton–Valentine leukocidin (PVL) gene. Logistic regression assessed associations with MDR. Of the 120 isolates examined, 55% were from hospital-acquired infections (HAI). The blaZ gene was present in 83.3% of isolates, and mecA in 36.7%. Genes tetK, tetM, ermC, and mphC were significantly associated with MDR. The PVL gene was detected in 18.3% of isolates. Approximately one-third of isolates met the definition of MDR, showing resistance to three or more antimicrobial categories. MDR in pediatric S. aureus in Egypt is primarily driven by genetic determinants, underscoring the significance of molecular surveillance and antimicrobial stewardship (AMS).