Background and Objectives: Staphylococcus aureus is a prominent component of the human flora; however, it can cause various pathological conditions. The emergence of methicillin-resistant S. aureus (MR-SA) has been significantly influenced by the overuse and inappropriate administration of antibiotics. The frequency of MR-SA nasal colonization among healthcare workers (HCWs) is increasing, and MR-SA is not restricted to hospital settings, with a notable rise in infections among individuals unrelated to HCWs. This study aimed to assess the prevalence of S. aureus nasal carriage among students at Government College University Faisalabad (GCUF), University of Agriculture Faisalabad (UAF), a Government School (GS), and a Private School (PS) to characterize the phenotypic traits of isolates and evaluate antimicrobial resistance profiles. Materials and Methods: A total of 1200 nasal swabs were inoculated on blood and mannitol salt agar, followed by phenotypic identification of S. aureus and MR-SA using biochemical tests. Antimicrobial susceptibility testing was conducted via the Kirby–Bauer disk diffusion method, and minimum inhibitory concentration (MIC) determination was performed using the broth dilution method. Additionally, nuc and mecA gene amplification through PCR aided in isolate identification. Results: The results revealed that 14% (168) of students harbored S. aureus in their nasal cavities, with 8.5% (102) carrying methicillin-sensitive S. aureus (MSSA) and 5.5% (66) carrying MR-SA. Male students exhibited higher S. aureus (57.7%) and MR-SA (21.4%) prevalence compared to females (42.3% and 17.9%, respectively). Urban students showed a higher S. aureus prevalence (54.2%), while rural students exhibited a higher MR-SA rate (22%). Overall, 80.3% of S. aureus isolates displayed resistance to erythromycin followed by fluoroquinolones (47.6%) and clindamycin (42.2%). All the S. aureus isolates, including MR-SA, remained susceptible to vancomycin and linezolid. PCR results revealed that 95.5% (63) of MR-SA isolates carried the mecA gene. Conclusions: The high prevalence of multi-drug-resistant (MDR) S. aureus raises significant public health concerns, with educational institutions potentially serving as reservoirs for bacterial transmission. The improper use of antibiotics contributes to bacterial resistance and increased infection rates. It is crucial to implement measures to prevent antibiotic misuse and develop comprehensive strategies within educational settings to effectively combat S. aureus and MR-SA prevalence.