Background Staphylococcus aureus (S. aureus) is a highly virulent pathogen that causes foodborne illness, food poisoning, skin and soft tissue infections, abscesses, mastitis, and bacteremia. It is common for meat and meat products to become contaminated with S. aureus due to dirty hands, food storage conditions, food production processes, and unhygienic conditions, causing food poisoning. Therefore, we aimed to detect virulence genes and S. aureus contamination in raw beef for retail sale. Methods In this study, samples of raw beef were collected from 100 retail market stalls in Ulaanbaatar. S. aureus was detected according to the ISO 6888-1 and ISO 6888-2:2003 standard, and the nucA gene encoding the species-specific thermonuclease was amplified and confirmed by polymerase chain reaction (PCR). In the strains of S. aureus found in the samples, the genes encoding the virulence factors sea, sed, tsst, eta, etb, and mecA were amplified and detected by multiplex PCR. Antibiotic susceptibility was determined by the Kirby–Bauer disc diffusion method. Results Thirty-five percent of the studied samples were contaminated with S. aureus. Antibiotic resistance was then assessed in these strains, and highest rates of resistance were determined to be to ampicillin (97.1%), oxacillin (88.6%), and penicillin (88.6%). Six virulence genes were detected by multiplex PCR in the S. aureus strains isolated from meat, and the penicillin-binding protein PBP 2A and its encoding gene mecA, enterotoxin A (sea), and toxic shock syndrome toxin (tsst) were identified in 17.1% of the samples. Moreover, cytotoxic toxin type a was identified in 5.7% of the samples, type b in 11.4%, and enterotoxin D (sed) in 2.9%. Conclusions The results show that S. aureus contamination is high in raw meat for retail sale, and the strains are resistant to antibiotics. These data indicate that there is a high risk for food poisoning caused by S. aureus in raw meat and that complications during its treatment are possible. S. aureus strains isolated from meat contain genes coding for both heat-resistant and nonresistant toxicity factors and are highly pathogenic, so it is necessary to ensure proper hygienic conditions during meat preparation and sale.