He played for the Los Angeles Dodgers, Philadelphia Phillies, Boston Red Sox, St. Louis Cardinals, and Florida Marlins in Major League Baseball (MLB).

He was originally selected in 1997 by the Boston Red Sox in the 45th round (1,332nd overall) of the 1997 MLB draft, but did not sign with them and instead went to Sacramento City College, for which he delivered the game-winning hit to lead the Panthers to the 1999 state championship.

Playing for the Las Vegas 51s of the AAA Pacific Coast League, Thurston hit .334 with an .878 OPS and 22 stolen bases in 2002, earning him the L.A. Dodgers' Minor League Player of the Year Award and Baseball America's AAA Player of the Year honors.

On December 1, he signed a minor league contract with the Washington Nationals that included an invitation to spring training.

He had his contract purchased by the big league club on July 27, 2007, after second baseman Chase Utley was placed on the disabled list.

On December 13, Thurston signed with the Boston Red Sox to a minor league contract with an invitation to spring training.

[9] On April 22, 2008, Thurston was designated for assignment and subsequently played in the Puerto Rican winter league in 2008 on a team managed by Eduardo Pérez.

Pérez was impressed with Thurston's versatility and thought his style of play would be a good fit with manager Tony La Russa of the St. Louis Cardinals.

Perez recommended Thurston to LaRussa,[10] and on December 16, 2008 he signed a minor league deal with the St. Louis Cardinals.

[18] Thurston played 58 games with the York Revolution of the independent Atlantic League in 2012, batting .314 with eight home runs and 28 RBI.

[23] Thurston was hired as a coach for the Portland Sea Dogs the Double-A affiliate of the Boston Red Sox for 2015.

On January 19, 2016, Thurston was named as the hitting coach for the Billings Mustangs the Rookie League affiliate of the Cincinnati Reds for the 2016 season.

On January 16, 2017, Thurston was hired as the hitting coach for the Modesto Nuts the Single-A affiliate of the Seattle Mariners for the 2017 season.