[1][3] Pitching for the baseball team, Thornton was All-State, all-California Interscholastic Federation (CIF), and all-Tri-Valley League.

[3][5][6] The San Francisco Giants selected Thornton in the 43rd round of the 2008 MLB draft, but he opted not to sign.

[3][8] In his senior year in 2010 he was 9–0 (his 9 wins matching the Oregon single-season record, and his 1.000 winning percentage setting the Oregon single-season record) with a 3.40 ERA (10th in the Conference) in 90 innings in which he struck out 73 batters and walked 16, and was named Pac-10 honorable mention.

[12][13][14] On November 30, 2012, the Athletics traded Thornton to the Pittsburgh Pirates in exchange for pitcher Chris Resop.

[12] He was a combined 7–3 with 5 saves and a 2.63 ERA, and recorded 90 strikeouts to 12 walks in 75+1⁄3 innings, as he kept opponents to a .204 batting average.

[12] On April 18, 2014, the Pirates traded Thornton and a player to be named later to the New York Mets in exchange for first baseman Ike Davis.

[20] Thornton pitched as a reliever for the Las Vegas 51s of the Triple–A Pacific Coast League, going 1–5 with a 4.22 ERA and 65 strikeouts in 59+2⁄3 innings.

[23] On May 30, 2017, Thornton signed with the Southern Maryland Blue Crabs of the independent Atlantic League of Professional Baseball.

On February 1, 2017, Thornton wrote on Twitter: "I'm excited to announce that I will be playing for Team Israel in the World Baseball Classic!