He came to prominence as a college football head coach at the Oregon Ducks from 2009 to 2012, leading them to the 2011 BCS National Championship Game.

Kelly's success led to a stint NFL, where he coached for four seasons, three with the Philadelphia Eagles (2013–2015) and one with the San Francisco 49ers (2016).

[6] Kelly, along with UNLV Rebels head coach Dan Mullen, former Winnipeg Blue Bombers offensive coordinator Gary Crowton, and Ohio State head coach Ryan Day, is part of the so-called "New Hampshire mafia" as they all have strong connections to New Hampshire.

[9] In 2008, the Ducks once again led the Pac-10 in scoring (41.9 ppg) and total offense (484.8 ypg), while breaking the school record marks set the previous season.

[11] Kelly became the first Pac-10 coach to win an outright conference championship in his first season, sending the Ducks to the Rose Bowl for the first time since 1995.

[15] In early October, Kelly led the team to a #1 spot on the AP, Harris, and USA Today Coaches Poll, followed a few weeks later by a #1 BCS ranking.

With Darron Thomas at quarterback and Doak Walker Award winner LaMichael James at running back, the Ducks averaged 49.3 points and 537.5 yards per game in the regular season.

[18] The Tigers, out of the Southeastern Conference, were coached by Gene Chizik, and had the Heisman Trophy winner at quarterback in Cam Newton.

A consecutive trip back to the BCS Championship appeared to be a strong possibility, but they were defeated 38–35 by #18 USC when an Oregon field goal attempt failed as time expired.

Led by redshirt freshman Marcus Mariota at quarterback and senior tailback Kenjon Barner, Oregon rolled to ten straight victories before finally falling to #14 Stanford in overtime 17–14 on November 17.

The Ducks proved to be too much for Kansas State as they prevailed in a 35–17 victory in Oregon's fourth consecutive year in a BCS bowl game.

[25] On April 16, 2013, The Oregonian reported that the University of Oregon had offered to put its football program on two years' probation in response to NCAA violations that allegedly took place during Kelly's tenure as head coach.

[26] On June 26, 2013, the NCAA Committee on Infractions issued its report concluding the investigation into Oregon's use of football scouting services.

In the spring of 2009, Jon Gruden and Kelly spent several days in Tampa, Florida, discussing theories, progressions, and offensive strategies.

[30] In January 2012, the Tampa Bay Buccaneers interviewed Kelly for the head coach position, but he declined to take the job since he had "unfinished business to complete" with the Ducks.

[32] Oregonian columnist John Canzano speculated that Kelly was waiting for the New England Patriots head coaching position to become available.

In early January 2013, numerous NFL teams expressed interest and Kelly was interviewed by the Buffalo Bills,[33] the Cleveland Browns[34] and Philadelphia Eagles.

In his second season in Philadelphia, Kelly finished with an identical 10–6 record, despite key injuries to players like quarterback Nick Foles and linebacker DeMeco Ryans.

On January 2, 2015, Eagles owner Jeffrey Lurie announced that Kelly would assume control of the 90-man roster (including authority over the draft and free agency), while Roseman would be "elevated" to the role of Executive Vice President of Football Operations, remaining in control of the salary cap and contracts.

[43] Soon afterward, the Eagles traded All-Pro running back LeSean McCoy to the Buffalo Bills for linebacker Kiko Alonso (who was a former Oregon Duck under Kelly) and Pro Bowl quarterback Nick Foles to the St. Louis Rams for quarterback Sam Bradford on March 10, 2015, under Kelly's request.

[46] On December 29, 2015, with the Eagles at 6–9, Kelly was fired before the final regular season game, in a statement made by Lurie.

[52] However, the 49ers went on a 13-game losing streak,[53] with many speculations opening up about trouble between Kelly and general manager Trent Baalke by April of 2016.

Those rumors ceased after the Ducks hired former South Florida Bulls coach Willie Taggart on December 7.

[66] In 2022, they began the season 5–0 for the first time since 2013,[67] and finished 9–4 (6–3 in the Pac-12) with a 37–35 loss to Pittsburgh in the Sun Bowl on a last-second field goal by the Panthers.

Kelly's Buckeye offense faced 4 of College Football's top teams and defeated Tennessee, Oregon, Texas, and Notre Dame en route to the schools 9th National Championship.

On February 4, 2025, the Las Vegas Raiders hired Kelly as their offensive coordinator under head coach Pete Carroll.

He lives in Los Angeles, California,[76] but has a small, tight-knit group of friends in Manchester, New Hampshire, who never speak about him to reporters.

[77] ESPN blogger Ted Miller describes Kelly as being "funny, biting, pithy, strange, fiery and surprising when talking to reporters.

[79][80] In 2009, Kelly responded to a season ticket holder's letter demanding a refund for his expenses after traveling to see Oregon's 19–8 loss to Boise State.

That loss ended with Ducks running back LeGarrette Blount responding to a Bronco player's taunts by punching him in the face.