Brad had a career year in with the Single A Augusta GreenJackets. His statistics included a 12-7 win-loss record, a 3.07 ERA, 126 strikeouts, and 55 walks in 27 games. The following year, Baker played for the Single A Sarasota Red Sox and went 7-9 with a 4.70 ERA and 103 strikeouts. He also played for Sarasota in , going 7-1, with a 2.79 ERA and 65 strikeouts, before being traded to the San Diego Padres on June 26, 2002 for Alan Embree. Just a few weeks after the trade, Baker was honored by being selected to play in the All-Star Futures Game at the MLB All Star Game. Baker finished the season with San Diego's AA affiliate, the Mobile BayBears. He would compile a record of 4-4, with a 4.48 ERA in 12 games with Mobile.