Infections due to Staphylococcus aureus are treated with antibiotics. Doctors try to determine whether the bacteria are resistant to antibiotics and, if so, to which antibiotics.

Infection that is acquired in a hospital is treated with antibiotics that are effective against MRSA. They include vancomycin, linezolid, tedizolid, quinupristin plus dalfopristin, ceftaroline, telavancin, or daptomycin. If results of testing later indicate that the strain is susceptible to methicillin and the person is not allergic to penicillin, a drug related to methicillin, such as nafcillin or oxacillin is used. Depending on how severe the infection is, antibiotics may be given for weeks.

MRSA infection can be acquired outside of a health care facility. The community-acquired MRSA strains are usually susceptible to other antibiotics, such as trimethoprim/sulfamethoxazole, clindamycin, minocycline, or doxycycline, as well as to the antibiotics used to treat MRSA infections acquired in the hospital.

Mild skin infections due to MRSA, such as folliculitis, are usually treated with an ointment, such as one that contains bacitracin, neomycin, and polymyxin B (available without a prescription) or mupirocin (available by prescription only). If more than an ointment is required, antibiotics effective against MRSA are given by mouth or intravenously. Which antibiotic is used depends on the severity of the infection and the results of susceptibility testing.