Objectives Methicillin-resistant Staphylococcus aureus (MRSA) causes severe infections with high mortality rates and health care costs. This study aimed to evaluate the prevalence of MRSA and its associated factors among patients with wound infections at Shaafi Hospital in Mogadishu, Somalia. Methods Wound swabs were collected from 418 patients with surgical wounds and cultured on Mannitol salt agar. S. aureus was identified using conventional methods, and antimicrobial susceptibility was performed using the disk diffusion method. Data analysis was conducted using SPSS software, with results presented as frequencies and percentages. Chi-square tests and binary logistic regression were performed to identify associations between MRSA and independent variables. Results S. aureus was isolated in 116 (27.8%) patients, with 31 (26.7%) cases identified as MRSA. The prevalence of MRSA was higher among females (10, 27%) than males (21, 26.6%). The most frequent MRSA was observed in the 21-30 years age group (13, 24.5%). Patients with deep wounds had a significant association with MRSA (adjusted odds ratio [AOR]: 4.32, 95% confidence interval [CI]: 1.042-17.92, P <0.044). Hospital stay of longer than 72 hours (AOR: 4.1, 95% CI: 1.22-13.80, P <0.022) and history of antibiotic use (AOR: 1.12, 95% CI: 0.17-7.15, P <0.018) were also found significant risk factors. Penicillin was 100% resistant to MRSA, followed by 58% to cotrimoxazole, 54.8% to gentamycin, and 51.6% to ciprofloxacin, whereas MRSA was 100% susceptible to vancomycin. Conclusions The prevalence of MRSA among inpatients with surgical wounds is considerable, with specific risk factors such as deep wounds, prolonged hospital stays, and previous antibiotic use significantly increasing the likelihood of MRSA infection. Antibiogram results indicated a significant resistance to frequently used antibiotics. This emphasizes the importance of implementing effective infection control measures and practicing antibiotic stewardship to manage MRSA in hospitals.