Seattle Mariners
Thomas was drafted by the Seattle Mariners as the 113th overall pick of the 2005 Major League Baseball draft. After signing with Seattle in June of that year, Thomas made his professional debut for the Everett AquaSox of the Low-A Northwest League.
In 2006, Thomas led all Mariners farmhands with 14 wins, finished second with 162 strikeouts and sixth with a 3.73 ERA. He was named the California League Pitcher of the Week in August and MiLB.com's Class-A Advanced Playoff Performer of the Year.
In 2007, Thomas was promoted to Double-A West Tenn Diamond Jaxx, but began the season on the disabled list with a strained left elbow. Upon being activated from the DL, Thomas struggled with control problems, posting a 4-9 record with a 5.51 ERA and a career high 61 walks.
In 2008, Thomas as he reduced his ERA with Double-A West Tenn to 4.32 and increased his strikeouts to walks ratio from 100 strikeouts/61 base on balls in '07 to 106 strikeouts/56 base on balls in '08. He was placed on the disabled list once again with a left hand laceration but came back to work out of the bullpen. Thomas received a mid-season call up to Triple-A Tacoma Rainiers posting a career low 3.71 ERA.
On September 1, 2008 the Seattle Mariners purchased Thomas' contract from Triple-A Tacoma. Thomas made his major league debut that day, taking on the Texas Rangers. In one inning of work, he gave up no runs, no hits, no walks, and struck out Marlon Byrd to end the game. Thomas pitched the rest of September with the Mariners, posting an 0-1 record and a 6.75 ERA.
In 2009, Thomas was re-signed by the Seattle Mariners to a one-year contract and was placed on the 40-man roster.