The patient was a 68-year-old male. At the previous hospital, continuous hemodiafiltration (CHDF)was performed through internal jugular vein for diabetic nephropathy. Long term catheterisation caused the abscess of the sternoclavicular joint, which induced methicillin-resistant Staphylococcus aureus( MRSA) empyema. Endoscopic thoracic debridement was performed for the empyema, however inadequate drainage for the abscess. Thereafter, the patient transferred to our hospital. We performed adequate drainage for the abscess under general anesthesia at 5 days after hospitalization, and then open decortication for empyema at 26 days. The patient recovered well after operation and was discharged from the hospital at 46 days. This was a successful case of surgical treatment for refractory MRSA empyema, which controls all focus of infection.