The Pirates drafted Mercer in the third round, with the 79th overall selection, of the 2008 MLB draft, choosing him as a shortstop. He began his professional career that season with the State College Spikes of the Class-A Short SeasonNew York–Penn League, before he was promoted to the Hickory Crawdads of the Class-A South Atlantic League. In 2009, Mercer played for the Lynchburg Hillcats of the Class-A Advanced Carolina League, finishing fifth in the Carolina League and second in the Pirates' farm system with 83 runs batted in. He was promoted to the Altoona Curve of the Double-A Eastern League in 2010. He began the 2010 season with Altoona, before receiving a promotion to the Indianapolis Indians of the Triple-A of the International League. The Pirates added him to their 40-man roster after the 2011 season to protect him from the Rule 5 draft. On May 29, 2012, the Pirates optioned Yamaico Navarro to Indianapolis and promoted Mercer to MLB. Mercer recorded his first MLB hit off Cincinnati Reds pitcher Johnny Cueto on May 30, 2012. Mercer got only 9 at-bats with the Pirates before being sent back to Indianapolis on June 24, 2012. On May 3, 2013, Mercer was called up from Indianapolis and led the Pirates to a 3–1 victory over the Washington Nationals with a two-run home run. On May 11, 2013 he had his first multiple home run game with two home runs against the New York Mets. Mercer was sent back to Indianapolis when Neil Walker was activated from the disabled list on May 13. Mercer was recalled on May 15 when John McDonald was placed on the disabled list. Mercer was named the new Pirates starting shortstop for the 2014 season, with Clint Barmes becoming his backup. In his first full season as a starter, Mercer hit.255 with 12 home runs and 55 RBIs in 149 games. Mercer competed with Korean rookie Jung-ho Kang for playing time in 2015. On July 19, 2015, Mercer suffered a leg contusion and sprained medial collateral ligament after being slid into a second base by Brewers outfielder Carlos Gómez. Mercer's season was cut short to 116 games, hitting.244 with 3 home runs. In 2016, he played in 149 games, establishing career highs in at bats, runs, RBIs and walks. The following season, Mercer hit a career high 14 home runs in 145 games. In 2018, Mercer was placed on the disabled list on August 16 due to a calf injury. He ended the season playing in 117 games, hitting.251 with 6 home runs. After the 2018 MLB season, and eleven years in the Pirates organization, Mercer became a free agent.
Detroit Tigers
On December 14, 2018, he signed a one-year $5.25 million deal with the Detroit Tigers. On April 13, 2019, he was placed on the injured list with a right quad injury. He was recalled on April 30, but went back on the injured list May 8 and did not return to major league action until July 1. Mercer was solid at the plate over the last two months of the season, hitting.342 in August and.302 in September, to finish the 2019 season at.270. He also had 9 home runs and drove in 22 runs in 256 at-bats. Mercer became a free agent following the 2019 season. On January 30, 2020, the Tigers signed Mercer to a minor-league contract with an invitation to spring training. Mercer was released by the Tigers prior to the 2020 season in March. Mercer re-signed with the Tigers on a minor league pact shortly after his release.
Personal
Mercer and his wife, Kacey, have two sons. Mercer grew up an Atlanta Braves fan.