Thayer was drafted out of high school by the Chicago Cubs in the 47th round of the 1999 Major League Baseball Draft, but did not sign. Thayer went undrafted out of Chico State in 2002, but was signed as a free agent by the San Diego Padres on September 25, 2002.\n', '

Thayer was used as a closer for the majority of his minor league career. In 2003, Thayer had 25 saves and a 2.06 ERA with the Class A Fort Wayne Wizards of the Midwest League. He began 2004 with the High-A Lake Elsinore Storm, where he had a 1.63 ERA and 23 saves, and was promoted to the Double-A Mobile BayBears in August. Thayer spent all of 2005 with Mobile, posting a 2.34 ERA and 27 saves in 56 games with 9.2 strike-outs per 9 innings. In 2006, he again spent the year with Mobile except for two appearances with Triple-A Portland in September. He had a 2.48 ERA and 27 saves in 57 games with Mobile.\n', '

Thayer was traded to the Tampa Bay Rays on September 15, 2006, as a player to be named later in exchange for Russell Branyan. He started 2007 with the Double-A Montgomery Biscuits and was advanced to the Triple-A Durham Bulls in August. He had a 2.35 ERA in 55 combined games for the year, finishing 47 of them. Thayer spent all of 2008 with the Bulls and pitched to a 2.77 ERA with 72 strike-outs in 68​1⁄3 innings and 9 saves in 52 games. Thayer again started 2009 in Triple-A Durham but made his Major League debut on May 22, 2009, at Land Shark Stadium in Miami Gardens against the Florida Marlins. He pitched 3 innings, allowing one earned run and collected his first Major League save. Thayer had 3 stints with the Rays in 2009, including a September call-up. He pitched in 11 games with the Rays, giving up 7 earned runs in 13​2⁄3 innings. At the Triple-A level in 2009, he posted a 2.27 ERA with 17 saves in 51 games. Thayer spent most of 2010 with Durham, where he had a 3.45 ERA in 46 games with 55 strike-outs in 60 innings. He was moved up to the majors on August 6, 2010, to add bullpen depth, but only pitched in a single game with the Rays before being sent back down. He was granted free agency at the end of the season.\n', '

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