Boone played baseball for the University of Southern California. In 1993, he won a Cape Cod Baseball League championship with the Orleans Cardinals and hit 15 doubles that summer (still a club record). The Cincinnati Reds selected Boone in the third round of the 1994 MLB draft. Boone made his debut in June 1997, and was ejected from the game after being
called out sliding into home.
On the last day of the 1998 season, the Reds started the only MLB infield composed of two sets of brothers; first baseman Stephen Larkin, second baseman Bret Boone, shortstop Barry Larkin, and third baseman Aaron Boone.