Background: Staphylococcus aureus is an important cause of neonatal infections, particularly in special care baby units (SCBU), where antimicrobial resistance poses growing challenges. This study aimed to describe the clinical presentations, burden, and antimicrobial resistance of Staphylococcus aureus infections in a Level II SCBU. Methods: A retrospective review was conducted of all microbiological samples yielding Staphylococcus aureus from neonates admitted to the SCBU between 1 November 2024 and 31 December 2025. Results: A total of 500 newborns were admitted to the SCBU during the study period. Fifteen (3%) microbiological samples were positive for Staphylococcus aureus, of which nine (67%) were methicillin-resistant Staphylococcus aureus (MRSA). Positive cultures included blood (n=4), eye swabs (n=9), and umbilical swabs (n=2). The most common clinical presentation was conjunctivitis (n=9), followed by sepsis (n=4) and umbilical discharge. 33% of the affected neonates were preterm, and 53% had low birth weight. 67% of the neonates had prior admission and treatment at SCBU before acquiring Staphylococcus aureus infection. All four cases of sepsis were late-onset neonatal sepsis, and three of these were caused by MRSA. Overall, the incidence of Staphylococcus aureus septicemia was 80/10,000 hospitalized infants. Among the MRSA septicemia cases, 2/3 isolates demonstrated resistance to clindamycin, cloxacillin, cotrimoxazole, and fusidic acid, with sensitivity only to vancomycin. No mortality was reported. Conclusion: Staphylococcus aureus, particularly MRSA, contributes significantly to late-onset infections in the SCBU, with conjunctivitis being the most common. High levels of antimicrobial resistance highlight the need for ongoing surveillance, strict infection control measures, and judicious antibiotic use.