Gordon attended the University of Nebraska–Lincoln and played third base. 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 hitting . 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, 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.