In August 2002, Bush appointed Brown to the Transition Planning Office for the new Department of Homeland Security, serving as the transition leader for the Emergency Preparedness and Response Division. As undersecretary, Brown also directed the National Incident Management System Integration Center, the National Disaster Medical System and the Nuclear Incident Response Team. After Bush announced the creation of the Department of Homeland Security, Allbaugh left government and Bush nominated Brown in January 2003 for the directorship of FEMA. Brown was sworn into his position on April 15, 2003.