Prior to that, Zimmer served as a defensive assistant for the Cowboys, Atlanta Falcons, and Cincinnati Bengals.

His college teammates were positively influenced by his constantly "up" attitude, especially during hot August pre-season double workouts.

In 2005, he implemented the 3-4 defense favored by head coach Bill Parcells, although Zimmer had no prior experience with it.

Zimmer coached in Atlanta for only one season after Petrino left the Falcons for the University of Arkansas after thirteen games.

[6] On January 15, 2014, Zimmer earned his first head coaching position when the Minnesota Vikings hired him to replace Leslie Frazier.

[8] At TCF Bank Stadium, the Vikings lost the wild-card playoff round to the Seattle Seahawks 10–9 while playing in subzero temperatures and the third-coldest game in NFL history.

Zimmer suffered a detached retina during the October 31, 2016 Monday Night Football game against the Chicago Bears.

On a windy night at Soldier Field, the edge of Zimmer's playcard, which was laminated, blew into his eye.

Zimmer underwent emergency eye surgery on November 30, 2016, forcing him to miss the Vikings' Thursday Night Football game against the Dallas Cowboys.

In the playoffs, the 2017 Vikings beat the New Orleans Saints in the divisional round with a last-second touchdown pass from Case Keenum to Stefon Diggs, which became known as the "Minneapolis Miracle".

[14] Hampered by injuries and opt-outs by many starting defensive players (including defensive end Danielle Hunter missing the entire 2020 season with a neck injury and new free-agent acquisition Michael Pierce opting out of the season due to COVID-19), the Vikings suffered a 'down year' with a 7–9 record in 2020, missing the playoffs and finishing third in the NFC North.

On January 10, 2022, Zimmer was fired as head coach of the Minnesota Vikings, ending his eight-year tenure with the team.

Three days later, Zimmer was awarded the game ball by Bengals head coach Marvin Lewis after the team's 17–14 victory over the Baltimore Ravens.