Lee was drafted by Florida Marlins with 12 pick in the eighth round of the 1997 Major League Baseball Draft by the Benton High School in his hometown of Bentonville, Arkansas, but instead chose to attend Meridian Community College in Mississippi. In 2002, Lee played for Double-A Harrisburg, and overall 7-2 record with a 3.23 ERA in the Eastern League played in the middle of summer.
Lee hit three games with the Akron Aeros before being promoted to Buffalo bison, Triple A affiliate in the Cleveland farm system. He struck again this season, giving up one run in five innings against the Kansas City Royals, resulting in a no decision for Lee, but a loss for the team. Lee suffered the groin strain during a spring training start, and forced him to start the regular season on the disabled list.
