Methicillin-resistant Staphylococcus aureus (MRSA) is a major hospital-acquired infection, yet its current epidemiology in Pakistan remains unknown. This study aimed to determine MRSA prevalence across wards in Peshawar’s Rehman Medical Institute. Microbiologic culture and susceptibility testing were performed on 160 total samples. S. aureus was isolated from 18 samples (11.3%), of which 17 (94.4%) were MRSA. Other pathogens like Enterococcus, Pseudomonas, Klebsiella, and Escherichia coli were also detected at lower frequencies. No bacterial growth occurred in 60% of tested samples. The extremely high MRSA positivity rate among isolated S. aureus demonstrates this multidrug-resistant strain is flourishing in the hospital and underscores the need for improved infection control. Continued surveillance of antibiotic resistance rates is vital to guide interventions against nosocomial MRSA transmission as a public health threat in Pakistan. Further studies should explore genetic and phenotypic bases of local MRSA strains to elucidate antibiotic evasion mechanisms and virulence traits. The study revealed a substantial 94.4% prevalence of MRSA in S. aureus positive samples from hospital patients, indicating antibiotic resistant strains now overwhelmingly dominate in this setting. Such extensive resistance has dire implications for treatment options and underscores how deeply entrenched MRSA has become within the hospital ecosystem, necessitating more aggressive infection control to protect public health.