Braun began 2006 playing for the A-Advanced Brevard County Manatees. He earned a spot in the Florida State League All-Star game, and played in the All-Star Futures Game. He was rated the top third base prospect in the FSL, and "Baseball America" rated him the best batting prospect in the league. On June 21, Braun was promoted to the Class AA Huntsville Stars (Alabama) of the Southern League. In July he was voted the Brewers' Organizational Player of the Month, and at the end of the season he was voted the sixth-best prospect in the Southern League. Collectively between Class A and Class AA, Braun finished with a .289 average, 22 home runs, 77 RBIs, and 26 stolen bases. He received the 2006 "Robin Yount Performance Award" as the Milwaukee Brewers Minor League Player of the Year.