Background/Objectives: Long-term data on the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) from the Western Balkans remain limited. This study investigated temporal changes in the molecular population structure and antimicrobial resistance of MRSA in Serbia over more than four decades. Methods: A total of 395 non-duplicate MRSA isolates from four temporally distinct collections (1975–1985, 1997–2003, 2009–2010, and 2018–2019) were analyzed. Isolates were characterized by antimicrobial susceptibility testing, spa typing, SCCmec typing, and detection of Panton–Valentine leukocidin (PVL) genes. Clonal complexes and putative MLST associations were inferred from spa repeat patterns and previously established molecular epidemiological associations rather than determined by direct MLST or whole-genome sequencing. Results: Marked differences in the molecular composition of MRSA were observed across the four collection periods. The 1975–1985 collection was dominated by isolates assigned to CC8-MRSA-I and ST239-related CC8-MRSA-III backgrounds. By 1997–2003, the early CC8-MRSA-I background was no longer prominent, while ST239-related CC8-MRSA-III and South German-related CC5-MRSA-I predominated. In 2009–2010, CC5-MRSA-I was the most frequently identified background, while ST239-related MRSA remained represented, and SCCmec IV/V-associated backgrounds were increasingly detected. By 2018–2019, greater molecular heterogeneity was observed, including a higher representation of CC45-MRSA-IV, changes in the distribution of CC5 backgrounds compared with the previously dominant CC5-t041-SCCmec I profile, continued detection of ST239-related CC8-MRSA-III, and an increased representation of ST152/CC152-associated isolates. PVL-positive isolates were absent from the first two collections, detected in 2009–2010 (4.0%), and more frequent in 2018–2019 (17.0%), predominantly within ST152/CC152- and CC1-associated backgrounds. Ciprofloxacin resistance increased from 0% in 1975–1985 to 84.0% in 2018–2019, while aminoglycoside resistance also increased markedly. Resistance to erythromycin and clindamycin remained consistently high, whereas no resistance to vancomycin, teicoplanin, or linezolid was detected among the investigated isolates. Conclusions: Over four decades, the investigated MRSA collections from Serbia showed substantial changes in molecular population structure, including the repeated detection of ST239-related MRSA, shifts in the predominant hospital-associated backgrounds, and greater molecular diversity in the later collections, with increased representation of SCCmec IV/V-associated and PVL-positive isolates. Historical population movements and healthcare connections within the former Yugoslavia may have contributed to the circulation of internationally recognized MRSA lineages in Serbia, although their role could not be directly established. Although the sampling design and typing resolution do not permit definitive conclusions regarding continuous clonal persistence or direct lineage replacement, these findings provide a valuable long-term perspective on MRSA molecular epidemiology in Southeastern Europe and highlight the importance of historical strain collections for investigating changes in antimicrobial-resistant bacterial populations.