As a freshman under head coach Lloyd Carr, Henson battled for the starting quarterback job against Tom Brady and ultimately was named the backup for the 1998 season.

The two players platooned during the season's first seven games, with Brady playing the first quarter, Henson the second and Carr then deciding upon a quarterback for the second half.

He missed the first 3 contests after having surgery on his right foot just prior to the start of the season on August 24, with redshirt freshman John Navarre replacing him.

[4] Henson threw for a career-high 312 yards in a road loss to #21 Northwestern, 54–51, and also tied a school record with four passing touchdowns.

In the regular season finale, Henson led the #19 Wolverines to Columbus to take on #12 Ohio State and threw again for over 300 yards en route to a 38–26 win.

Henson left prior to his senior season after signing a six-year, $17 million baseball-only deal with the New York Yankees on March 25, 2001.

He finished the summer with the Reds' AA affiliate in Chattanooga, hitting .172 (11-for-64) with one home run and 9 RBIs in 16 games, before returning to football practice at Michigan.

Frustrated by his lack of progress and in need of a third baseman at the major league level, the Yankees acquired Aaron Boone at the 2003 trading deadline.

[8] Boone eventually hit a pennant-clinching home run against the Boston Red Sox in the 2003 postseason, but then injured his knee in a pickup basketball game during the offseason.

[17] It was later reported that owner/general manager Jerry Jones influenced the organization into making the transaction, becoming part of a string of young quarterback acquisitions that were also former baseball players (Quincy Carter and Chad Hutchinson).

After the surprising release of starter Carter on August 4, Henson began the first 6 games of the season as the third-string quarterback behind Tony Romo.

In the tenth game against the Baltimore Ravens, he replaced an injured Testaverde in the fourth quarter, completing all of his 6 passes for 47 yards and one touchdown.

On Thanksgiving Day, Testaverde had previously missed practice and was limited with a sore right shoulder, so Henson was given the chance to start his first NFL game against the Chicago Bears, making 4 out of 12 completions for 31 yards, driving the offense for a touchdown on the Cowboys' first possession, but also had one interception that was returned 45 yards for a touchdown in the second quarter.

With the score tied at 7, head coach Bill Parcells opted to insert Testaverde in the third quarter and the team went on to win the contest 21–7.

Henson returned to third-string in the fifteenth game against the Philadelphia Eagles, finishing the season with 10 out of 18 completions for 78 yards, one touchdown and one interception.

In 2005, Henson had a poor training camp showing and landed third on the depth chart behind Drew Bledsoe and Tony Romo.

He was declared inactive for all 16 games and at the end of the season, Parcells announced that Henson would be allocated to NFL Europe league to work on his skills.

Henson was promoted to the active roster on October 12 when quarterback Jon Kitna was declared out for the team's Week 5 contest with an injury.

Shortly after the signing of quarterback Daunte Culpepper, Henson was waived by the Lions on November 12 when the team claimed wide receiver Adam Jennings off waivers from the Atlanta Falcons.