After failing to receive an NFL contract, Nagy joined the Arena Football League (AFL), where he spent six seasons playing for the New York Dragons, Carolina Cobras, Georgia Force, and Columbus Destroyers.

[4][5] In 1994, Nagy led the Barons to the Pennsylvania Interscholastic Athletic Association (PIAA) Class AAA playoffs, where they reached the semifinals against the Berwick Bulldogs.

While the Barons primarily used the veer running offense, head coach Mike Williams elected to switch to a pass-heavy system for the Berwick game to surprise the Bulldogs.

[19] Ginn and Nagy shared the starting job to open the 1998 campaign, but the former broke his leg in the third game of the year against West Chester and was unable to play for the remainder of the season.

Nagy made a limited return the following week against Rhode Island, entering the game during the third quarter, where he failed to complete each of his four pass attempts before being substituted for Mike Medley in the final period.

After Ginn was briefly knocked out of the game, Nagy filled in early in the fourth quarter and threw a 22-yard touchdown pass to Butter Pressley to put the Blue Hens up 45–24.

[27] Nagy ended the season with 3,436 passing yards, setting a school record that stood until Joe Flacco eclipsed the mark in 2007, and a program-best 29 touchdown throws.

[31][32] Later auditions with the Jacksonville Jaguars, Dallas Cowboys, and New York Jets – the third coming after beginning his arena football career in 2002 – and a phone conversation with Minnesota Vikings officials also failed to result in contracts.

There, he caught the eye of head coach John Gregory,[35] who likened Nagy to his former Iowa Barnstormers star and Pro Football Hall of Fame quarterback Kurt Warner as the two were comparable in size, possessed the ability to throw while running, and shared similar leadership qualities.

[40] In June, Kanell's struggles against the Orlando Predators prompted Nagy to return to action in the fourth quarter, where he threw a 12-yard touchdown to Jason Maxwell for his lone score in the 52–33 loss.

[43] During the offseason, Nagy tore his anterior cruciate ligament (ACL) during a flag football game in Lancaster, Pennsylvania that prevented him from playing the 2003 season.

[35] While rehabilitating his leg alongside trainer Steve Saunders,[44] Nagy also spent the year receiving his real estate license and working as a substitute PE teacher.

[49] After Carolina dropped to 3–7, including winning only one of their last eight games, Gregory was replaced by defensive coordinator Ron Selesky,[50] while Rickey Foggie became the starting quarterback for the rest of the season.

[30][61] Despite his club's struggles, Nagy broke franchise single-season records in completions and attempts (372 for 527), passing yards (4,265), and touchdowns (85), and led the league in passer rating (125.5).

[30] The Force qualified for the playoffs and played the Dragons in the first round, where Nagy completed 28 of 39 of this throws for 362 yards and ten total touchdowns, nine of which came by passing, as Georgia won 72–69.

[74] After trailing 35–21 during the second quarter, the Destroyers scored 31 of the game's next 34 points, while Nagy was 20 for 32 for 285 yards and six touchdowns (four passing, two rushing) as Columbus upset Dallas 66–59 to make their maiden Conference Championship appearance.

[66] For the 2008 season, head coach Doug Kay elected to have Nagy play and serve as the de facto offensive coordinator, but the Destroyers struggled mightily as they opened the year 1–4.

The following year, he was invited to serve the same position at Cedar Crest High School in Lebanon, Pennsylvania, where his wife, Stacey, was the girls' track coach.

[44] On August 10, three days before their preseason game against the New England Patriots, backup quarterback Kevin Kolb suffered a knee injury; to avoid putting stress on starter Donovan McNabb and third-string A. J. Feeley, the Eagles attempted to sign Nagy as a player.

[90] After a 4–12 campaign in 2012, Reid was fired by the Eagles and moved to the Kansas City Chiefs,[91] bringing Pederson and Nagy with him as offensive coordinator and quarterbacks coach, respectively.

[109] They defeated the Green Bay Packers on December 16 to improve to 10–4, as Nagy became the second Bears' rookie head coach in team history to win 10 games, joining George Halas in 1920.

[116] Nagy also became the fifth coach in team history to record at least 12 wins in a season, joining George Halas, Mike Ditka, Dick Jauron, and Lovie Smith.

[117] After the 2018 season, Fangio departed the Bears to become the Denver Broncos head coach; to replace him, Nagy hired Chuck Pagano as defensive coordinator.

[129] Following Trubisky's departure via free agency, the 2021 season began with Andy Dalton as the Bears' starting quarterback over first-round rookie Justin Fields, while Nagy promoted safeties coach Sean Desai to defensive coordinator after Pagano retired.

On October 25, Nagy tested positive for COVID-19, resulting in special teams coordinator Chris Tabor assuming head coaching duties for Week 8 against the San Francisco 49ers.

[135] In a statement released following his dismissal, Nagy thanked the team "for the opportunity to lead one of the game's most storied franchises" and described his stint as "four years I'll always remember.

[146] Quarterback struggles and defenses playing further back in coverage, which he respectively experienced with the Bears and Chiefs, prompted Nagy to gradually shift toward shorter passes in what he nicknamed a "touchdown to checkdown mentality.

Player archetypes and West Coast plays such as the bubble screen and hot read are based in arena football strategy, while his preference to throw deep to stretch the defense is influenced by the indoor sport's tendency to do the same.

"[168] When Nagy's firing loomed in December 2021, Chicago Sun-Times writer Rick Morrissey explained "the Bears fell in love with a person, not a football coach.

"Sweep the Sheds" is a phrase from the James Kerr book Legacy, which follows the New Zealand national rugby union team; after games, the All Blacks clean their locker room as an act of humility.