Canadian Football League In January 1990, Hufnagel was hired by new Calgary Stampeders head coach,
Wally Buono, to be the team's quarterbacks and running backs coach. By March, he had been given the title of
offensive coordinator. In June 1994, Hufnagel added Assistant Head Coach to his title. Under Hufnagel's tutelage, the five- and six-receiver package became a staple in Calgary's offence. In 1994, Calgary set CFL records for points scored one season (698), touchdowns one season (82), and touchdowns passing one season (52). Future
Pro Bowler quarterbacks
Doug Flutie and
Jeff Garcia earned All-CFL honors. In 1994,
Allen Pitts set a CFL record for receiving yards in a season (2,036). Receiver
Dave Sapunjis was the
CFL's Most Outstanding Canadian twice (1993 and 1995). In 1995, Pitts and Sapunjis both caught 100 passes.
Arena Football League and CFL In 1997, Hufnagel became
head coach and
general manager of the
Arena Football League’s
New Jersey Red Dogs. In two seasons there, he posted a 17–11 record. In the second half of both the
1997 and
1998 CFL seasons, the BC Lions brought Hufnagel in as a consultant to help with their offence.
National Football League After two seasons (
1999,
2000) as the quarterbacks coach for the
Cleveland Browns, Hufnagel was named the quarterbacks coach of the
Indianapolis Colts, where he coached
Peyton Manning to a 62.7 percent completion percentage and for 4,131 yards passing. He spent the 2002 season as the quarterbacks coach on
Tom Coughlin’s staff in
Jacksonville. That year, quarterback
Mark Brunell threw only seven
interceptions in 416 pass attempts, and an 85.7
quarterback rating. He spent the 2003 season with the
Super Bowl champion
New England Patriots. Under Hufnagel's tutelage,
Tom Brady earned a second
Super Bowl MVP award, completing 60.2 percent of his passes for 3,620 yards and 23 touchdowns. Hufnagel became the offensive coordinator of the New York Giants in
2004, and molded them into one of the NFL's most potent offenses.
Tiki Barber set a franchise rushing record two years in a row, and the Giants became only the fifth team in NFL history to have five different players score at least seven touchdowns. (Tiki Barber,
Jeremy Shockey,
Plaxico Burress,
Amani Toomer and
Brandon Jacobs). While Hufnagel is credited with the rapid development of quarterback
Eli Manning, he is sometimes criticized for his often predictable play-calling and an inability to utilize his offensive play-makers effectively. During the
2006 season, Hufnagel came under much criticism for being too pass-happy and abandoning the running game after the Giants trailed during games. In addition, he was also questioned for having Manning throw the ball the third and sixth most passes in the league over 2005 and 2006 despite Tiki Barber clearly being the best player on offense. In addition, his situational play-calling came under scrutiny, such as when running back Brandon Jacobs was removed from the game inside the five yard-line in two games, thus making the offense more predictable to opposing defenses. Following a 30–7 defeat by the New Orleans Saints, Hufnagel was stripped of his duties as offensive coordinator. A week later, it was revealed he was fired.
Return to the CFL During the BC Lions' 2007 training camp, Hufnagel served as a guest coach. On December 3, 2007, Hufnagel was hired as the head coach and general manager of the Calgary Stampeders. In his first season, he led the Stampeders to the
Grey Cup title with a 22–14 victory over the Montreal Alouettes on November 23. For his performance in the
2008 CFL season, he was awarded the
Annis Stukus Trophy as the CFL's coach of the year. On March 29,
2012, the Stampeders announced that Hufnagel had agreed to a five-year contract extension. That year, he guided the Stamps back to the Grey Cup game. The Stampeders lost the
100th Grey Cup game to the
Toronto Argonauts 35-22. In the 2013 CFL season, Hufnagel and the Stampeders finished the season with a league-best 14-4 record. They lost the Western Final to Saskatchewan. The
following season, Hufnagel led the Stampeders to a 15-3 record, the top record in the CFL once again. In the playoffs, the Calgary Stampeders faced the Edmonton Eskimos (who previously eliminated Saskatchewan) and defeated them 43-18, leading them to Calgary's second Grey Cup in three years. They would face the Hamilton Tiger-Cats in the
102nd Grey Cup and win the game 20-16 for Calgary's seventh Grey Cup championship. Following the Stampeder's championship season of 2014, Hufnagel was awarded the Annis Stukus Trophy as the CFL coach of the year for the second time in his career. On December 3, 2014, Hufnagel announced that the
2015 season would be his last in coaching. In 2016, the plan was for offensive coordinator
Dave Dickenson to take over as head coach, with Hufnagel continuing as general manager. In week 17 of 2015, Hufnagel reached 100 wins as a head coach and as a general manager. When he left coaching, Hufnagel was the second-winningest head coach in Stampeders history, trailing only Buono. He was also tied with
Bud Grant as the
ninth-winningest coach in CFL history (102 wins), and had the most wins of any coach, along with Grant, who spent his entire CFL coaching career with just one team. In January
2016, Hufnagel was named president of the Stampeders, and continued as general manager. Calgary went to the next three Grey Cup games, winning in
2018. Prior to the
2023 season, Hufnagel stepped down as general manager, and the position was given to Dickenson. Hufnagel gained 175 wins as Calgary's general manager, which placed him fourth all-time in CFL history. He retained his position as team president and added football operations consultant to his title. On January 23,
2024, the Stampeders announced that Hufnagel would remain with the organization and assume the role of special advisor to
Jay McNeil, the football club's new president, and to Dickenson, the football club's general manager and head coach. On December 4, 2025, it was announced that Hufnagel had joined the
Toronto Argonauts as a senior advisor to the general manager and head coach. He was inducted into the
Canadian Football Hall of Fame as a builder in 2020.
CFL coaching record ==Personal life==