Persistent Staphylococcus aureus bacteremia is frequently defined as bacteremia persisting for ≥7 days despite proper antibiotic therapy. Its treatment includes removal of all infection foci and proper antibiotic therapy. Vancomycin remains the antibiotic of choice in MRSA bacteremia. Alternative agents, linezolid or daptomycin, are available, but a consensus regarding management of persistent MRSA bacteremia on vancomycin failure is still lacking. We report a case of a 60-year-old male who received thoracoabdominal aorta replacement operation due to dissecting aneurysm of the ascending and descending aorta. Surgical site infection and bacteremia caused by MRSA occured, and wound debridement operations were performed. The patient was treated with vancomycin in therapeutic doses but MRSA bacteremia persisted for 168 days in a row. Although the inserted aortic graft was the most probable source of persistent bacteremia, surgical removal was impossible. Linezolid was administered as an alternative antibiotic but had to be discontinued from time to time due to thrombocytopenia induced by this agent. In the end, MRSA bacteremia was successfully managed by alternating vancomycin-linezolid therapy.