The New York Yankees selected Flores in the ninth round of the 1997 Major League Baseball Draft. In 2001, the Yankees sent him to the Texas Rangers to complete a trade earlier in the year for infielderRandy Velarde. Flores made his major league debut with the Rangers on April 23, 2002. He also played for the Colorado Rockies before signing as a free agent with the Cardinals on November 20, 2003. Flores won a championship ring when the Cardinals won the 2006 World Series, defeating the Detroit Tigers four games to one. He appeared in seven games in that postseason, registering innings without giving up an earned run. The next season, he appeared in a career-high 70 games, posting 55 innings pitched and a 4.25 ERA. From 2005 through 2007, he appeared in 185 games, contributing a pivotal role in the Cardinals' bullpen. However, injuries in the second half of 2007 began to reduce his effectiveness, and in the summer of 2008, he cleared waivers prior to a demotion to the Memphis Redbirds. Flores became a free agent after the 2008 season. On February 10,, Flores signed a minor league contract with the Colorado Rockies with an invitation to spring training. He spent most of the season with the Colorado Springs Sky Sox before the Rockies called him up in September when the rosters expanded. He made the Opening Day roster in 2010 and appeared in 47 games, completing innings with 18 SO and a 2.96 ERA, a record of 2–0, and a 1.28 WHIP. Left-handed batters collected 11 hits in 50 at bats against him. The Rockies designated him for assignment on August 19, 2009. The Minnesota Twins claimed him off waivers six days later. On February 10, 2011, he signed a minor league contract with the San Diego Padres with an invite to spring training. Working innings for Tucson, he struck out 19 and walked six before opting out of his contract on May 15. Two days later, he signed a minor league contract with the Yankees. He was released by the Yankees on August 2, 2011 and immediately signed a minor league contract with the Milwaukee Brewers. He was released by the Milwaukee Brewers on Tuesday, August 30, 2011, after asking for his release.
Post-playing career
In 2012, Flores joined ESPN as an on-air analyst during the NCAA Division I Baseball Championship. In 2013, Flores returned to USC as a baseball broadcaster and later assistant baseball coach, while also pursuing a master's degree. In 2014, Flores earned a Master of Science degree in post-secondary administration with an emphasis on athletic administration. In February 2015, Flores joined the Pac-12 Network as a baseball analyst. He launched his own startup company, OnDeckDigital, which utilizes video capture technology to allow players and scouts to evaluate their game play. Scouting departments of MLB clubs started using his product. On August 28, 2015, the Cardinals hired Flores as their new director of scouting, replacing Chris Correa.
Personal life
Flores' brother, Ron, was also a left-handed relief pitcher who appeared in the major leagues, playing for the Oakland Athletics from 2005–07. Flores and his wife, Lindsey, have two daughters and one son.