Johnson accepted a football scholarship from the University of Wisconsin–Madison along with his cousin Ben Johnson. As a redshirt freshman, he appeared in 7 games, playing mainly on the field goal and extra point conversion lines. He became a starter at center in the second game of his sophomore season, when All-American Casey Rabach was moved to right guard. He started every game as a junior. He was named team captain and received second-team All-Big Ten honors as a senior.
One of the priorities in Bill Parcells first season as the head coach of the Dallas Cowboys was improving the center position play. To that end, he made Andre Gurode concentrate on playing guard and selected Johnson in the second round of the 2003 NFL Draft. In training camp he was named the starter, but suffered a right knee injury during a practice that required microfracture surgery, which was thought to be career-threatening, because at the time not many players fully recovered from this medical procedure. In 2004, Tyson Walter was named the starter at center, but suffered a sprained left knee in the second quarter of the season opener against the Minnesota Vikings, opening the door for Johnson to start in the rest of the games. The next year, after facing competition in training camp from Gurode, he went on to start all 16 games, but still split time at center. In 2006, he lost the starting position to Gurode, who went on to become a Pro Bowler. The Cowboys didn't re-sign him in free agency at the end of the season.
Arizona Cardinals
On March 5, 2007, the Arizona Cardinals signed him to a contract as a free agent. He started 14 games at center, as part of an offensive line that allowed the team's fewest sacks in 20 years and that helped Edgerrin James rush for 1,222 yards. In the 2008 off-season, Johnson underwent two surgeries on his left knee and was placed on the injured reserve list. On October 21, he was released with an injury settlement, after the team couldn't reach an agreement to restructure his contract.
Miami Dolphins
On November 29, 2008, Johnson was signed by the Miami Dolphins, reuniting with Bill Parcells, who was the Executive Vice President of Football Operations. He played as a reserve center and guard in only four games, because he experienced recurring problems with his left knee.
In 2013, Johnson was hired as the offensive coordinator at Southern Door High School. In 2014, he was an assistant football coach and offensive coordinator at NCAA Division III St. Norbert College. He also was an assistant coach at Southern Door High School in Brussels and a morning show personality on WQDC, which he owned. In 2016, he joined the University of Wisconsin football staff as an assistant offensive line coach. In December 2017, he was named the head football coach at East Central University in Ada, Oklahoma.
