Thompson, 24, is 4-7 with a 3.57 ERA (35 ER/88.1 IP) in 16 starts for Double-A San Antonio this season.
The Colorado native began the year allowing two earned runs or less in seven of his first eight starts. In 88.1 innings, he has allowed 84 hits, walked 41 and struck out 59.
He has a career minor league record of 38-33 with a 3.54 ERA (265 ER/673.2 IP) in 124 games (122 starts). Thompson was selected by the Padres in the fifth round of the 2002 First-Year Player Draft.
Thompson will report to Triple-A Omaha of the Pacific Coast League and be used out of the pen. He has been a starter throughout his career in the Padres organization.
Thompson was a frequent contributor to MadFriars.com with his 'Thompson's Tuesday's' prospect journal.