Methicillin-resistant Staphylococcusaureus (MRSA) has become a major public health problem all over the world. After the 2019 coronavirus illness (COVID-19), the pandemic may have influenced research priorities and resource allocation, potentially affecting the ability to monitor MRSA trends. The study aimed to evaluate the prevalence of S. aureus, including MRSA infections, and their antimicrobial susceptibilities over the years 2019 and 2020 in a tertiary hospital in Makkah City, KSA. A total of 2128 and 1515 laboratory (lab) samples were collected during the years 2019 and 2020, respectively. From these samples, the prevalence of S. aureus, including MRSA, and their antibiotic susceptibility were identified using standard, automated, and molecular microbiological methods. The present study shows that the lab prevalence ofall S. aureus during 2019 was found to be 35.5%, of which MRSA was 44.8%. During 2020, the frequency of S. aureus strains was 16%, of which MRSA was 41.2%. The most common MRSA isolated during both years were colonizing pus swabs and urine samples. The results showed that MRSA susceptibility against antimicrobial agents in 2019 was as follows: vancomycin (100%), linezolid (100%), trimethoprim-sulfamethoxazole (88%), and doxycycline (34.2%). The MRSA strains isolated during 2020 were as follows: vancomycin (100%), linezolid (96%), trimethoprim-sulfamethoxazole (100%), and doxycycline (24.3%). There was no significant difference in the incidence and antimicrobial resistance rates of MRSA over the two years. It was concluded that the prevalence rates of MRSA have not increased in 2020 when compared to 2019. Vancomycin, linezolid, trimethoprim-sulfamethoxazole, and doxycycline remain susceptible to the positive collected MRSA strains. There was no significant difference between the prevalence and antimicrobial resistance rates of MRSA between 2019 and 2020. Continued research efforts are needed to address this persistent public health threat. Strategies to control the spread of MRSA should include early detection of MRSA and surveillance, even during pandemics.