Hernández was signed as a non-drafted free agent by the Atlanta Braves on September 16, 2000. He spent five seasons in the Braves' minor league organization, but only played 19 games for their AAA affiliate, the Richmond Braves, before moving to Baltimore.
Baltimore Orioles
Hernández was claimed off waivers by the Baltimore Orioles on October 12, 2006. He made his major league debut for the Orioles as a late-inning defensive replacement July 8, 2007 against the Texas Rangers. Luis collected his first major league hit, a double, in his second career game on July 12, 2007. The game was played at Camden Yards, against the Chicago White Sox. Hernández got his hit, a line drive to center field, off of the first pitch he saw from White Soxrelief pitcherDewon Day in the bottom of the ninth inning. He also got his first major league RBI on the play, as Jay Gibbons came in to score. His first major league home run was hit on September 27, 2007 against the Toronto Blue Jays. Hernández was penciled in as the Orioles' starting shortstop for the 2008 season, but faced Spring Training competition from Brandon Fahey. Considered an "all-defense" player, Hernández and Fahey vied for the position vacated by Miguel Tejada, who was traded to the Houston Astros over the offseason. He became a free agent at the end of the season.
In November, Hernández signed a minor league deal with the Kansas City Royals. He added to the major league roster on May 3, 2009. On July 6, 2009, he was designated for assignment to make room for the newly acquired Ryan Freel. Hernández was released on January 19, 2010.
The Mets purchased Hernández's contract from the Buffalo Bisons on August 27, 2010. Hernández played in seventeen games for the Mets in 2010, hitting two home runs with six runs batted in. His season ended after hitting a foul ball off his right foot, breaking a bone in his foot on September 18, although he still managed to hit a home run on the next pitch. On Oct. 17, 2011, he declared for free agency.
Texas Rangers
On Dec. 1, 2011, he signed a minor league contract with the Texas Rangers. Hernández spent most of 2012 with Triple-A Round Rock, hitting.262/.303/.376 with 8 HR and 70 RBI in 129 games as the team's shortstop. Hernández did play 2 games with the Rangers, going 0-1 in each, coming in as a defensive replacement.
On March 29, 2016, Hernández signed with the Bridgeport Bluefish of the Atlantic League of Professional Baseball. On November 1, 2017, Hernández was drafted by the New Britain Bees of the Bridgeport Bluefish dispersal draft. On February 20, 2018, Hernández signed with the Bees for the 2018 season.
Post Playing Career
However, Hernández later announced his retirement prior to the season on April 21, 2018, in order to pursue a coaching opportunity in the Kansas City Royals organization.