Gordon struggled at the beginning of the 2009 season, hitting just 2-for-21 (. 095) with one home run and three RBIs in seven games before being injured while sliding. He underwent surgery on April 17 to repair a tear in the labral cartilage of the right hip, and was on the disabled list for twelve weeks. After playing a few games in the minors, Gordon came off the disabled list and rejoined the Royals on July 17 going 1 for 4 against the Tampa Bay Rays. Gordon stole home for the first time in his career on August 2 against the Rays, becoming the first Royal to do that since Mendy López in 2003. The Royals optioned Gordon to the Triple-A Omaha Royals on August 18 to free up a roster space for Kyle Farnsworth. Gordon had a batting average of . 198 at his demotion, and had made five errors while appearing in only 29 games. After Omaha finished up its season, Gordon returned to the Royals in September. Between the return to Kansas City and the end of the season, Gordon got a hit in 15 of the final 20 games he played in, and hit home runs in back-to-back games against the Minnesota Twins.