[4] Thornton made his professional debut with the Single-A Everett AquaSox in the Northwest League, recording a 27.00 ERA in two games.

[5] In 1999 and 2000, Thornton was a starting pitcher with the Single-A Wisconsin Timber Rattlers in the Midwest League, and showed improvement with his ball control and accuracy, striking out nearly one batter per inning.

In 2001, Thornton had a breakout year for the Single-A San Bernardino Stampede in the California League, where he posted a 14–7 record in 27 starts, along with a stellar 2.52 ERA and 192 strikeouts in only 157 innings pitched.

He started only four games, but posted an incredible 0.36 ERA, with a 3–1 record, gave up only eight hits in 25.1 innings of work and struck out 18 batters.

[5] Thornton stayed with the Tacoma Rainiers in 2004 and posted a 7–5 record in 16 games (15 starts), along with a 5.20 ERA and 74 strikeouts in 83 innings pitched.

[5] Thornton made his MLB debut on June 27, 2004, with the Mariners in a game against the San Diego Padres, pitching brilliantly over four innings, only allowing three hits and striking out one batter.

[6] Throughout the season, the Mariners used Thornton for mostly middle reliever duty, except for one game on July 10, when he started on against the Chicago White Sox.

[8] On March 20, 2006, Thornton was traded from the Seattle Mariners to the Chicago White Sox in exchange for outfielder Joe Borchard.

[8] After participating in the 2009 World Baseball Classic, representing the USA,[citation needed] Thornton made 70 MLB appearances in 2009, going 6–3 with four saves and a 2.74 ERA.

[13] For the rest of the 2013 season with the Red Sox, Thornton's playing time was limited due to an oblique strain, but he made 20 appearances out of the bullpen, going 0–1 with a 3.52 ERA.

On March 3, 2016, Thornton signed a minor league deal with the San Diego Padres with an invitation to Spring training.

[21] Since transitioning to the bullpen with the White Sox, Thornton has scrapped his secondary pitches and now relies heavily on a mid- to upper-90s four-seam fastball.