Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is an emerging bacterium associated with a much higher incidence of clinical infection worldwide than any other strains of S. aureus. The misappropriation of non-prescribing drugs amongst university students in Pakistan has become a severe problem. The present study aims to evaluate the nasal carriage rates of Staphylococcus aureus and methicillin resistant Staphylococcus aureus (MRSA) in university students and described the history of associated risk factors. Among the 350 samples, 300 (85.71%) were S. aureus positive and 50 (14.28%) were other isolates. The positive individual includes 295 (98.33%) males and 5 (1.66%) females. A total of 16 (5.3%) S. aureus out of the total 300 were resistant to cefoxitin (MRSA) and 284 (94.66%) isolates were MSSA (Methicillin Susceptible Staphylococcus aureus). The strains were confirmed by the amplification of nuc gene analysis as S. aureus and the MRSA was confirmed with mecA gene analysis. All the samples were catalase positive, whereas 72.33% was coagulase positive and 27.66% were found as coagulase negative. Among the coagulase positive 7.37% were resistant to methicillin. The antibiotic resistance patterns showed no MRSA isolates to be resistant to Vancomycin and Linzolids. In most cases the MRSA was less susceptible to other antibiotics. It was concluded that Vancomycin and Linzolid can be used as drug of choice as no MRSA was found resistant to them. Furthermore, molecular PCR diagnosis is suggested as rapid and sensitive technique for the identification of MRSA isolates based on their mecA gene analysis.