Methicillin Resistant Staphylococcus aureus (MRSA) is a major health problem worldwide. Diseases caused by these microorganisms most often are difficult to treat consequently, present with severe outcomes. Despite the increase association of MRSA in most hospital acquired infections, surveillance systems to control the spread of these infections are lacking especially in the developing countries. The present study is part of a major study developed to trail the incidence of multidrug resistant pathogens in clinical settings using available resources, with the aim to gather relevant data for the management and control of nosocomial infections. The specific objective of the current study is therefore to determine the prevalence and antimicrobial susceptibility of MRSA isolates from one of the largest hospitals in the country. This was a hospital based cross sectional study involving 114 participants, conducted between March and June 2016. Various clinical specimens were inoculated on to blood agar and mannitol salt agar and incubated at 35-37°C aerobically for 18-24 hours for the isolation of S. aureus. Isolates were identified using the catalase and coagulase tests. Sensitivity testing was done using the Kirby Bauer disk diffusion method. Data were analysed using SPSS version 20.0. Out of 114 samples analysed, S. aureus was isolated from 33 (28.95%) while MRSA was detected in 15 (13.16%). Antimicrobial susceptibility testing revealed high resistance (80-100%) to penicillins and no resistance to amikacin, lincomycin and ofloxacin. Multidrug resistance to at least three antibiotics was also observed among MRSA isolates. MRSA and multidrug resistant S. aureus are common in the study site. Therefore, there is a need for the improvement of surveillance systems to monitor and curb the spread of these resistant pathogens.