As there is no effective treatment against hemorrhagic fever with renal syndrome (HFRS), the development of effective vaccine is important. An inactivated hantavirus vaccine (IHV) has been used in Korea, but there has been controversy regarding its effectiveness. We conducted a case-control study to evaluate the vaccine effectiveness (VE) of IHV against HFRS in the Korean military. Unadjusted and adjusted VEs of IHV were 59.1% and 58.9%, respectively. VE was higher in divisions with high incidence of HFRS (unadjusted VE, 71.4%; adjusted VE, 78.7%). Our study demonstrated the moderate effectiveness of IHV in high-risk populations residing in endemic area.