Millwood made his debut as a pitcher for the Atlanta Braves on July 14, 1997. He had is best year in 1999, winning eighteen games and losing seven. He formed a part of the Atlanta Braves' star pitching rotation, which also consisted of Greg Maddux and Tom Glavine, which was regarded by many as the best in the National League.
In 2002, after having another eighteen-win season, the Braves traded Millwood to the Phillies for the catcher Johnny Estrada, probably in order to cut their payroll in the midst of economic difficulties. In 2003, Millwood fared reasonably with the Phillies, winning fourteen games. In that year, he also pitched a no-hitter against the San Francisco Giants.