After redshirting the 2005 season, Wilson played in 10 games and finished 10th on team with 41 tackles, 0.5 tackles for loss, five pass breakups, one forced fumble, one fumble recovery and an interception. He started final five games at cornerback and delivered an impressive performance at the 2007 Fiesta Bowl, finishing with 10 tackles in Boise State's 43–42 upset win over Oklahoma. Wilson was named honorable mention Freshman All-America by Sporting News.

As a sophomore, Wilson started all 13 games at cornerback, finishing the season with 41 tackles, eight pass breakups, two interceptions, two tackles for loss, one sack and a blocked kick. His season-high six tackles came against East Carolina in the 2007 Hawaii Bowl. Wilson earned second-team All-WAC honors.

In his junior season, Wilson led Boise State with five interceptions, 10 pass breakups and 15 passes defended. He recorded 35 tackles, 26 of which were unassisted, and returned 33 punts for 470 yards and three touchdowns. Wilson started each game of the season, making his current streak of 31 consecutive starts the longest active streak on team. He was named first-team All-WAC cornerback and second-team all-conference punt returner. Also, The Sporting News named him to their 2008 All-American Second-team.

In 2009, Rivals.com listed him at No. 3 of their preseason cornerback power ranking. In October, he was named a midseason All-American by The Sporting News, and in early November he was named one of twelve semifinalists for the 2009 Jim Thorpe Award.

Wilson was considered one of the best cornerbacks available in the 2010 NFL Draft, and drew comparisons to Dré Bly. According to Sports Illustrated′s Tony Pauline, Wilson was "graded as a fringe middle round pick by NFL scouting services" prior to his senior season, "but has since cemented himself as a top 100 choice." He was only the second defensive back from Boise State to be selected in the first three rounds of an NFL Draft, following Gerald Alexander in 2007

Wilson was taken in the 1st Round with the 29th overall pick by the New York Jets. At the 2010 Jets minicamp, Wilson impressed the coaching staff, many of whom considered Wilson a "steal."

On July 31, 2010, Wilson signed a five-year, $13 million contract with the Jets. He served as the #3 CB behind Darrelle Revis and Antonio Cromartie going into training camp.

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