Methicillin-resistant Staphylococcus aureus (MRSA) is responsible for serious threats to human health, causing various syndromes worldwide. Here, our purpose was to estimate the prevalence of nosocomial MRSA among isolates from King Khalid Hospital (KKH) and Maternity and Children Hospital (MCH) at Hafar Al-Batin Governorate, Saudi Arabia, and to determine the resistance of these isolates to common antibiotics used for treatment. One-hundred clinical specimens were collected from admitted patients during a six month period, and subjected to MRSA screening using traditional microbiological techniques. Antimicrobial susceptibility testing (AST) was also performed and confirmed by the VITEK2 automated system. Among the 37 S. aureus strains isolated from KKH, 23 (62.16%) were identified as MRSA. In MCH, 38 (60.31%) out 63 isolated strains were identified as MRSA. According to AST, few MRSA strains were resistant to teicoplanin, fosfomycin, linezolid, and mupirocin in both hospitals. Vancomycin resistance was not detected in any of the MRSA strains. Twelve MRSA strains from KKH and 17 strains from MCH were considered multidrug resistant (MDR). In conclusion, prevention is critical to reduce the high prevalence of MRSA.