In 2005, Nolan was hired as the head coach of the San Francisco 49ers, following in his father's footsteps, the former San Francisco 49ers and New Orleans Saints head coach, Dick Nolan. He also served as his own general manager. Nolan and the 49ers selected Alex Smith with the first overall pick in the 2005 NFL Draft. Nolan thought Smith to be cerebral, introspective, and non-confrontational. Nolan also evaluated Aaron Rodgers but did not believe that Rodgers' attitude could co-exist with him. Nolan finished the 2005 season with a 4-12 record. Nolan led a late season run and the 49ers improved in 2006 to 7-9. That led to expectations for the 2007 season, which included at least 9 wins and a playoff appearance. The season started well at 2-0, but an 8-game losing streak ended all hope of a playoff run. During the season, he publicly disagreed with Smith over the severity of the quarterback's shoulder injury. Nolan had been under intense scrutiny in the Bay Area. After the season, Nolan lost his general manager position and on October 20, 2008, Nolan was fired and replaced by his assistant head coachMike Singletary.
Denver Broncos (second stint)
In early 2009, Nolan was hired by the Denver Broncos as the defensive coordinator under head coach, Josh McDaniels. With a new 3-4 defense the Denver Broncos gave up the fewest points in the NFL during the first six games of the season, and made their way to their first 6–0 start since the 1998 season in which they won Super Bowl XXXIII. The Broncos went 2 and 8 the rest of the way, and missed the playoffs. On January 18, 2010, Mike Nolan and Josh McDaniels mutually decided Nolan would resign as the defensive coordinator of the Denver Broncos.
Miami Dolphins
On January 19, 2010, Nolan was hired by the Miami Dolphins as defensive coordinator.
Atlanta Falcons
On January 17, 2012, Nolan was hired by the Atlanta Falcons as defensive coordinator.
San Diego Chargers
In 2015, Nolan was hired by the San Diego Chargers as their linebackers coach.
New Orleans Saints
In 2017, Nolan was hired by the New Orleans Saints as their linebackers coach.
On January 5, 2020. Nolan was hired by the Dallas Cowboys as their defensive coordinator.
Suit issue
Following his hiring by the 49ers, Nolan asked the NFL for permission to wear a suit and tie on the sidelines as a tribute to his father. The league initially denied Nolan's request because of the contract it had with Reebok for its coaches to wear team-logo attire, a ruling that was changed during Nolan's second season as coach. In the new NFL policy, coaches were allowed to wear a full suit for only two home games per season. The suits were designed, marketed and labeled under the Reebok corporation. Nolan debuted the suit in a game at home against the Seattle Seahawks on November 19, 2006. A day later, Jacksonville Jaguars head coach Jack Del Rio sported another Reebok suit on Monday Night Football. After further lobbying by Nolan, the NFL and Reebok reached an agreement to allow suits to be worn at all home games in the 2007 season. After his firing from the 49ers, however, he has simply worn team-issued apparel in all subsequent coaching jobs.
