We report a case of Vibrio vulnificus sepsis developed during deferoxamine therapy for transfusional iron overload due to secondary hemochromatosis of myelodysplastic syndrome. The patient was treated with adjuvant deferasirox in combination with ciprofloxacin, after rapid diagnosis of V. vulnificus sepsis using real-time polymerase chain reaction (PCR). This case suggests that since V. vulnificus DNA can be detected by real-time PCR for several days even after patients receive antibiotics, real-time PCR for V. vulnificus is a very useful test for establishing an early diagnosis, even if a patient has been treated with antibiotics prior to admission.