On June 16, Holt hit for the cycle against the Atlanta Braves at Fenway Park. He doubled, singled, and hit a home run off of Julio Teherán, and completed it with a triple in the 8th inning off of Sugar Ray Marimón. In doing so, he became the first Red Sox player to accomplish the feat in 19 years, since John Valentin in 1996.

Holt graduated in 2006 from Stephenville High School in Texas. In 2003, his freshman year, he made the District 8-4A All-District baseball team despite batting just .227, and shared the league’s Newcomer of the Year award. Holt was a second-team All-District 8-4A inclusion his sophomore year, batting .324 for the season. In 2005, Holt was named defensive player of the year in District 6-4A, and he earned all-district honors in 2006, his senior year.

Holt attended Navarro College in 2007 and 2008. After transferring to Rice University in 2009, he posted a .348 batting average with 12 home runs and 43 RBIs in 59 games for the Rice Owls. He also led the Owls with 67 runs scored and shared the team lead with 11 stolen bases. In the same season, he was named both to the All-NCAA Regional Team and the All-Silver Glove Trophy Series team.

Holt was drafted by the Pittsburgh Pirates with the club’s ninth round selection in the 2009 Major League Baseball Draft, one pick before his Rice teammate Ryan Berry.

Holt began his professional career with the Pittsburgh Pirates’ short season, Class-A affiliate, the State College Spikes, before advancing to the High-A Bradenton Marauders in 2010. His 2010 season was cut short due to injury to his medial collateral ligament, which required surgery. He began the 2011 season with the Pirates’ Double-A affiliate, the Altoona Curve. On July 13, 2011, Holt was named the MVP of the Eastern League All-Star Game after hitting a two-run homer in the ninth inning.

Holt opened 2012 with Altoona and later joined Triple-A Indianapolis Indians. He was promoted to the Pittsburgh Pirates from the minors as the major league rosters expanded on September 1.

Holt made his Major League debut on September 1, 2012. At the time of his promotion, he had hit a .322 average in 102 games with Altoona and .432 in 24 games for Indianapolis.

On December 26, 2012 Holt was traded to the Boston Red Sox (along with Joel Hanrahan) for Jerry Sands, Stolmy Pimentel, Mark Melancon, and Iván DeJesús, Jr.. Holt started the 2013 season with the Triple-A Pawtucket Red Sox. He debuted for Boston after getting called up on July 6 in Anaheim. In 2013, Holt played in 26 games, hitting .203 with 11 RBI. The Red Sox finished the year 97–65, clinching the AL East division. Holt was not active in the playoffs, but the Red Sox went on to win the 2013 World Series.

Holt married Lakyn Pennington on November 9, 2013. The couple have 2 sons, Griffin Wyatt Holt, born in December 2016 and Rippkin Penn Holt in September 2020. Holt worked with The Jimmy Fund, serving five consecutive seasons as Jimmy Fund captain for the Red Sox, to assist with fund raising and cancer awareness.

In 2015, Holt made the opening day roster for the first time in his career.

For the 2015 regular season, Holt appeared in 129 games, batting .280 with two home runs and 45 RBIs. Defensively, he played 58 games at second base, 35 games in the outfield, 33 games at third base, 11 games at shortstop, 8 games at first base, and one game as designated hitter.

Following the announcement that Wade Boggs’s number 26 was to be retired, Holt switched his jersey number to number 12 in 2016. On May 15, Holt was ejected for the first time in his career by home plate umpire and crew chief Joe West for arguing balls and strikes. On May 19, Holt suffered a concussion and was placed on the disabled list. On August 24, Holt returned to the Red Sox, covering third base. For the 2016 regular season, Holt appeared in 94 games and finished with a .255 batting average, 7 home runs, and 34 RBIs.

In the 2016 American League Division Series between the Red Sox and Indians, Holt was named the starting third baseman over Travis Shaw. He batted .400 with a home run and an RBI as Cleveland swept Boston in three games.

Holt again spent time on the disabled list in 2017, due to a concussion and the effects of vertigo. After playing on April 20, Holt was out of the Red Sox lineup until July 16. During the 2017 regular season, Holt appeared in 64 games, batting .200 with no home runs and seven RBIs.

In the 2017 American League Division Series against the Houston Astros, Holt played only in Game 2, pinch running and then staying in the game as second baseman; he did not have a plate appearance.

On February 19, 2020, Holt signed a one-year contract with the Milwaukee Brewers that included a club option for 2021. He was designated for assignment on August 22, 2020, after hitting .100/.222/.100 with 9 strikeouts over 39 plate appearances.

Holt signed with the Washington Nationals on August 29, 2020.