Mangini worked his way up in the NFL under the tutelage of Bill Belichick. He began his career as a ball boy with Cleveland at the age of 23, and later became an intern in the public relations. While working as a ball boy, he was often quoted as saying "no job is too small in the NFL." He worked 18 hours a day in the PR department, and at night he took copies of stats in the copyroom. Bill Belichick, at the time the head coach of the Cleveland Browns, found him there, and liked him so much that he asked the general manager if they had another job for him. Mangini was given the smallest coaching job in the Browns, putting film together for the coordinators.
On September 10, 2006, Mangini made his regular season debut as head coach. The Jets were the victors in a 23-16 road win against the Tennessee Titans. Mangini was shortly after nicknamed the Penguin by Jets wide receiver Laveranues Coles. He is one of four head coaches to have a winning record in his first season with the Jets (Bill Parcells, Al Groh, and Herman Edwards are the others). Mangini finished his rookie season with a 10-6 record, the same as former Jets coach Herman Edwards did in his rookie year. Edwards received a higher salary after the playoffs.
The Jets clinched an AFC wild card spot on December 31 by beating the Oakland Raiders at home by the score of 23–3, in the final game of the regular season. They would later go on to lose the Wild Card playoff game, 37–16, to the New England Patriots under Bill Belichick. Nevertheless, it marks a turn around orchestrated by the Jets and often injured quarterback Chad Pennington who overcame all odds after sustaining two rotator cuff injuries. Pennington finished the season setting career marks in yards, completions, and attempts, earning him honors as the 2006 NFL Comeback Player of the Year.
In recognition of the success Mangini had in his first season as head coach of the Jets, he was named 2006 AFC Coach of the Year at the NFL 101 Awards.
The second year (2007) under Mangini was less fruitful for the Jets, who went 4–12 during the regular season, failing to qualify for the play-offs.
Mangini also had a cameo in an episode of the mob drama The Sopranos.
Mangini is also known for naming his children after important figures in his career as a professional football coach. His son Zack was born on Brett Favre's 39th birthday, and Mangini had promised Favre that he would name his son after the legendary quarterback should he choose to sign with the Jets. As such, Mangini's third son is named Zack Brett. In addition, his first son, Jake Harrison, is named after New England Patriots safety Rodney Harrison, and his middle child is named Luke William after Patriots head coach Bill Belichick.
| Team | Year | Regular Season | Post Season | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Won | Lost | Ties | Win % | Finish | Won | Lost | Win % | Result | ||
| NYJ | 2006 | 10 | 6 | 0 | .625 | 2nd in AFC East | 0 | 1 | .000 | Lost in Wild Card Round |
| NYJ | 2007 | 4 | 12 | 0 | .250 | 3rd in AFC East | - | - | - | - |
| NYJ* | 2008 | 2 | 2 | 0 | .333 | 3rd in AFC East | - | - | - | - |
| NYJ Total* | 16 | 19 | 0 | .441 | 0 | 1 | .000 | |||
| Total* | 16 | 19 | 0 | .441 | 0 | 1 | .000 | |||