Historically, native populations in the Republic of Djibouti have experienced only low and unstable malaria transmission and intermittent epidemics. In recent years, efforts at malaria control have been aggressively pursued. This study was performed to inform revised malaria prevention recommendations for military service members and international travelers to the country. Laboratory-confirmed cases of malaria documented at large medical facilities and within military and civilian health care systems in the Republic of Djibouti from 1998 to 2009 were reviewed. In recent years, fewer than 5% of febrile cases among the three largest passive surveillance systems were laboratory-confirmed as malaria, and incidence of confirmed malaria was well below 1/1,000 persons/year. As efforts in the Republic of Djibouti progress toward elimination, and in conjunction with continued efforts at surveillance, emphasizing mosquito-avoidance measures and standby emergency treatment will become reasonable recommendations for malaria prevention.