Fleck will receive a five-year deal at Minnesota, the school announced Friday. The contract is worth $18.5 million, according to the Minneapolis Star Tribune.
"It is with mixed emotions that I announce my decision to leave Western Michigan University for the head football coaching job at the University of Minnesota," Fleck said in a statement to WMMT in Kalamazoo, Michigan. "Although I am grateful for and excited about this opportunity, this was a very difficult decision to make; one that involved much introspection and prayer. Heather and I love Kalamazoo and the Western Michigan University family of staff, students, alumni and fans. I simply feel called to take on this new challenge and to start a new chapter in my family's journey. I am proud of what we have accomplished together in Kalamazoo. I feel we have left WMU football in a much better place than when we arrived here. That was our mission. I'll always be your fan and friend. RTB PJ."
Fleck and former LSU coach Les Miles both interviewed for Minnesota's vacant coaching job in the past few days, sources told ESPN's Brett McMurphy.
Minnesota fired coach Tracy Claeys on Tuesday, just over two weeks after the football program became embroiled in a standoff with administration over the suspension of 10 players in connection with allegations of sexual assault.
Athletic director Mark Coyle said he made the decision to fire Claeys to "address challenges in recruiting, ticket sales and the culture of the program. We need strong leadership to take Gopher football to the next level and address these challenges."
Coyle promised to quickly find a replacement for Claeys despite this being late in college football's hiring season. He needed a coach to plunge into recruiting and address the deep divisions between the players that remain and the school's administration. Coyle and university president Eric Kaler flew to Chicago on Wednesday for meetings. The two sides reached an agreement two days later.
In a statement Friday, Coyle called Fleck "a proven winner and a strong leader."
"He's built a unique, positive culture that gets the best out of his students on the field and in the classroom," Coyle said of Fleck. "His infectious energy and passion make him a terrific coach and dynamic recruiter. I am excited he will be leading the Gophers for years to come."
Now Fleck has little time to waste in beginning to repair a fractured program.
Players threatened in December to boycott the National Funding Holiday Bowl after expressing reservations about the university's investigation that led to the suspension of their teammates.
Some were accused of pressuring a woman into sex during a party after the team's season-opening win over Oregon State. Many of those players continue to be upset with Coyle and Kaler for how the situation was handled, and Coyle acknowledged his frustration over federal privacy laws that prevented him from communicating more with a confused team.
That issue isn't going away soon, with appeals hearings for the 10 players expected to be held this month.
"I get they're upset. I get they're frustrated. I understand that," Coyle said Tuesday. "It's our job to find a leader who will take this program forward and unite all of them in one direction, one goal."
One underclassman Gophers player told McMurphy he wasn't sure whether the players would embrace Fleck.
"Guys don't want to take it out on the new staff, but we still really don't like the administration," the player said.
The 36-year-old coach is 30-22 in four years at Western Michigan, with three bowl appearances. His relentless, youthful energy and motivational team motto "Row the boat!" helped push the Broncos into the national spotlight this fall, with the campus and city of Kalamazoo abuzz over a program that had never before won more than nine games in a season.
Fleck, a star receiver at Northern Illinois who played briefly in the NFL for the San Francisco 49ers, has been an assistant coach at his alma mater, Ohio State, Rutgers and in 2012 for the Tampa Bay Buccaneers before taking over the Broncos.
Mid-American Conference coaches have been plucked by Big Ten teams several times before, with mixed success at best. Tim Beckman started at Illinois in 2012 after leaving Toledo, and he was fired after a 12-25 record over three seasons amid allegations of player mistreatment. Darrell Hazell left Kent State to join Purdue in 2013. The Boilermakers went 9-33 before he was fired halfway through his fourth season.
Ohio State's Urban Meyer launched his career at Bowling Green, but he had stops at Utah and Florida in between. Jerry Kill, the predecessor to Claeys, left Northern Illinois for the Gophers six years ago and went a respectable 29-29 before epilepsy forced his retirement.
When Coyle announced his decision to fire Claeys, who led the Gophers to a 9-4 record and a win over Washington State in the Holiday Bowl, the athletic director was applauded by victims' rights advocates and many academics at the university for responding emphatically to troubling allegations.
He was also criticized by some donors, alumni and players for reacting too harshly after Hennepin County twice cited a lack of evidence as the reason for declining to press charges.
The Gophers reached out to Penn State offensive coordinator Joe Moorhead but were turned down early in the process, two people with knowledge of the situation told The Associated Press. They spoke on condition of anonymity because Minnesota was not commenting publicly on its search.
"I think we all need to take a deep breath," Coyle said Tuesday. "We'll go out; we'll find a great football coach for the University of Minnesota. We'll have a chance to move forward in a positive direction.
Information from The Associated Press was used in this report.