He played in Major League Baseball (MLB) for the Tampa Bay Rays, New York Mets, and San Diego Padres.

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.

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 was traded to the Tampa Bay Rays on September 15, 2006, as a player to be named later in exchange for Russell Branyan.

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 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.

[4] As part of the move, the Mets brought up Ángel Pagán and sent down Fernando Martínez and Pat Misch.

Thayer was sent down to the minors on June 11 after pitching in 4 games, as D. J. Carrasco was brought back up after being demoted in April.

Thayer signed a minor league contract with the San Diego Padres on December 6, 2011.