The Red Sox drafted Lester in the second round (No. 57 overall) of the 2002 First Year Players Draft and gave him the highest signing bonus of any second-rounder that year, $1 million.

Lester quickly moved through the Red Sox organization, posting an 11-6 record, a league-leading 2.61 ERA and a league-best 163 strikeouts for the AA Portland Sea Dogs in 2005. He was named Eastern League Pitcher of the Year and Red Sox Minor League Pitcher of the Year and was selected as the left-handed pitcher on the Eastern League's year-end All-Star team and on the year-end Topps AA All-Star squad.

On September 1^st, 2006, doctors confirmed that Lester had a treatable form of anaplastic large cell lymphoma. On December 5, 2006, Lester's latest CT Scan showed no signs of the disease, which appeared to be in remission. Lester attended spring training in 2007, and on March 5, 2007, he made his first appearance in a game. He retired all 3 batters he faced, with a total of 8 pitches. As of June 11, Lester was removed from the disabled list, and sent to Pawtucket for further rehab outings. Lester made his first 2007 start for the Boston Red Sox on July 23 against the Cleveland Indians, pitching 6 innings, allowing 2 runs on 5 hits and struck out 6, picking up the win. To honor Lester's comeback from lymphoma, Major League Ball honored him with the 2007 Tony Conigliaro Award.

In the 2007 World Series, Lester won the series-clinching Game Four for the Red Sox, pitching 5⅔ shutout innings, giving up just 3 hits and 3 walks while collecting 3 strikeouts. Lester became just the 3^rd pitcher in World Series history to win the series clinching game in his first post-season start.