Schoomaker served as the Commanding General of the Joint Special Operations Command from July 1994 to August 1996, followed by command of the United States Army Special Operations Command at Fort Bragg, North Carolina through October 1997. His most recent assignment prior to assuming duties as the Army Chief of Staff was as Commander, United States Special Operations Command at MacDill Air Force Base, Florida, from November 1997 to November 2000. According to the 9/11 Commission, Schoomaker wanted to take action against Al Qaeda in Afghanistan using his special operators but was unable to gain approval for the mission.