Gordon was a member of the 2004 U.S. National Team which had players from 15 different colleges. He helped lead Team USA to an 18–7 overall record, seeing the majority of his playing time at first base. He hit .388 with 4 home runs, 12 RBI and 18 runs scored in 24 contests and was named the top offensive player at the World University Baseball Championship in Tainan, Taiwan after leading all players with a .524 average (11-for-21) with 2 homers, 5 RBI and 8 runs scored in 8 games.
Gordon attended the University of Nebraska. In his junior year in 2005, he swept the collegiate baseball awards for college player of the year, winning the Dick Howser Trophy, Golden Spikes Award, the Brooks Wallace Award, and the ABCA Rawlings Player of the Year, he was also an ESPY Award Finalist for the Best Male College Athlete. He earned 1st-team All-America honors for the 2nd straight season going .372 (94–253) in 72 games with 22 doubles, 4 triples, 19 home runs and 66 RBI. Gordon was also 23 for 26 in stolen base attempts, and drew 63 walks, compared to 38 strikeouts, helping lead the Huskers to the 2005 Big 12 regular season and tournament titles and the school's 3rd College World Series appearance. He posted a .353 career average, where he hit 44 homers and drove in 189 runs, drew 139 walks and struck out just 106 times and was only the 2nd 2-time 1st-team All-American in Nebraska history. He finished the season as the Big 12 leader (conference games) in walks and on-base percentage, while ranking 3rd in home runs, total bases and slugging percentage, Gordon was the highest draft pick out of Nebraska since Darin Erstad was taken 1st overall in the 1995 draft.
He was named the No. 1 college draft prospect by Baseball America as well as the 2nd-best overall prospect, best pure collegiate hitter, the 2nd-best collegiate 5-tool talent, 2nd-best collegiate power hitter, best collegiate strike-zone judgment and 2nd-closest to the Majors among collegiate players.
Gordon declined to play for Team USA in 2006, while leading the Wichita Wranglers to the Texas League playoffs. He performed exceptionally well in his first full minor league season, winning the Texas League Player of the Year awarded to the best player award and Baseball America's Minor League Player of the Year award.
Gordon struggled to begin with, but the Royals stayed patient with him. He was hitting .185 with 3 home runs and 8 RBI through the first two months as an everyday starter of the regular season. However he was hot in June, batting .327 with 3 home runs and 14 RBI. He stayed consistent through the summer, hitting .253 in July, and .271 in August. However, he slumped to a .244 average for the final month of the season.
The Royals placed Gordon on the 15-day disabled list on August 23 because of a torn muscle in his right quadriceps. He was hitting .254 and was second on the team with 14 home runs, but also had club-high 109 strikeouts.
Gordon made the most errors (16) and had the lowest fielding percentage (.955) of all AL third basemen in 2008.
Gordon struggled in the beginning of the 2009 season, hitting just 2-for-21 (.095) with one homer and three RBIs in seven games. Gordon was injured on April 11 in a game against the New York Yankees when he slid into second base on a force play. 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, Alex came off the designated list and rejoined the Royals on July 17 going 1 for 4 against Tampa Bay. Alex stole home for the first time in his career on August 2 against the Rays becoming the first Royal to do that since Mendy Lopez in 2003. The Royals optioned third baseman Alex Gordon  to Triple-A Omaha on August 18 and reinstated reliever Kyle Farnsworth from the 15-day DL to take his spot on the active roster. After Omaha finished up its season, Gordon returned to the Royals in September.
Gordon began the 2010 season on a minor league rehab assignment with Class-A Advanced Wilmington, following a broken thumb suffered in Spring Training. Gordon was activated from the disabled list on April 17. He was demoted to the minor leagues in May, where he played left field. Gordon was recalled from Triple-A on July 23, 2010, to take the place of David DeJesus in the Royals' outfield, who was placed on the disabled list with a right thumb sprain.
In spring training in 2011, he led the major leagues in RBIs, with 23. Gordon finished 3rd place behind Paul Konerko and Victor Martinez in the American League Final Vote for the All-Star game with a .299 average to start the year. He broke the Royals single season record and is leading the majors in outfield assists. He is also second in the majors in doubles, with teammate Jeff Francoeur.
In 2011, he led all major league outfielders in assists, with 20. On November 1, 2011 it was announced that Alex had won his first American League Gold Glove for left fielder.
On February 9, 2012, Gordon signed a one-year, $4.775 million deal with the Royals to avoid arbitration. In the process, Gordon filed for $5.45, while the Royals countered with $4.15. He can earn $25K if he reaches 700 plate appearances, putting him at the original midpoint. However, on March 30, Gordon signed a four-year, $37.5 million extension with the Royals with a player option for 2016, becoming the third Royal player to sign an extension in the offseason. Gordon will earn $6 million in 2012, $9 million in 2013, $10 million in 2014 and $12.5 million in 2015. He would earn another $12.5 million should he accept his option for 2016. Gordon was set to hit the open market after 2013.
In 2012, Gordon won a Fielding Bible Award as the best fielding left fielder in MLB. He also won the Rawlings Gold Glove.
Gordon finished the 2012 season with a .294 batting average and led the majors with doubles, totaling 51 doubles.
Gordon shortly after gained distinction through his baseball card in 2006. Topps issued Gordon's rookie card prematurely, as only players on 25-man rosters or who have played in at least one Major League game are eligible. As a result, Topps stopped producing the card and cut holes in some of the existing cards. Examples that found their way into retail stores have garnered bids in the thousands of dollars on eBay.