Kelly received 25 votes from the AP college football poll panel. Penn State's Bill O'Brien was second with 14 votes. Stanford's David Shaw (four), Texas A&M's Kevin Sumlin (three), Kansas State's Bill Snyder (two) and Alabama's Nick Saban (one) also received votes.
Kelly is the first Notre Dame coach to win the AP award, which started in 1998.
Of course, the Irish haven't played for a national championship since 1988 and spent much of the past two decades trying to find a coach who could restore a program that was becoming a relic of its proud past.
After two seasons with Notre Dame, Kelly decided he wasn't spending enough time doing the best part of his job: coaching players. Kelly changed that in 2012, and he shuffled his staff. Then, with Kelly more in tune to his team and the assistants in sync with the head coach, Notre Dame went from unranked to top-ranked.
"When you're talking about the coach of the year, there's so many things that go into it," Kelly said. "I know it's an individual award and it goes to one guy, but the feelings that I get from it is you're building the right staff, that you've got the right players and to me that is a validation of the program. That you put together the right business plan."
He arrived in 2010 after two decades spent climbing the coaching ladder and winning big everywhere he worked. But in the world of college football, Notre Dame is a long way from Grand Valley State -- where Kelly won Division II national titles -- and Cincinnati, his previous stop, for that matter.
"I think the job tends to distract you," Kelly said earlier this week. "There are a lot of things that pull you away from the primary reason why you want to be head coach of Notre Dame, and that is graduate your players and play for a national championship.
"Now, to do that you have to have the pulse of your football team and you've got to have relationships with your players. If you're already going around the country doing other things other than working with your football team, it's hard to have the pulse of your team."
Kelly said he made a point of spending more time with the team this year.
"That's why I got into this. I want to develop 18 to 21 year olds. My development as the head coach at Notre Dame this year has been about getting back to why you would want to coach college players. You want to learn about them; you want to know their strengths and weaknesses; you want to help them with leadership skills; you want to help them when they're not feeling confident in their ability.
"For me, that is why it's been the most enjoyable year as the head coach at Notre Dame, is that I got a chance to spend more time with my team."
The first step, though, toward a successful 2012 season for Notre Dame can be traced to Feb. 10. On that day Kelly announced his coaching staff. The most notable change was moving Chuck Martin from defensive backs coach to offensive coordinator to fill the hole left when Charley Molnar became the coach of Massachusetts.
Martin was defensive coordinator for Kelly at Grand Valley State, then replaced his boss as head coach of the Division II power when Kelly was hired by Central Michigan after the 2003 season.
The move might have seemed odd to some, but Kelly, who built his reputation on offensive acumen, wanted a right-hand man who understood exactly what he wanted.
To replace Martin on the defensive side, Bob Elliot was hired from Iowa State to coach safeties. Harry Hiestand was hired away from Tennessee to replace offensive line coach Ed Warinner, and co-defensive coordinator Bob Diaco, who had been with Kelly at Central Michigan and Cincinnati, was promoted to assistant head coach.
"The voice of your coordinators has got to be in lock step with the head coach," Kelly said. "Now both of these guys have been with me a long time.
"Chuck Martin on offense, I wanted a voice that went back with me to Grand Valley State. And with Bob Diaco someone that goes back to Central Michigan with me. So yeah, it was important to get that voice right."
The last change Kelly needed to make involved Xs and Os. Kelly wanted to win now, but with a first-year starter and redshirt freshmen at quarterback. He had to adjust his style.
Out went the push-the-pace offense that had helped him reach two BCS games at Cincinnati. In came a more deliberate approach.
"We conduct the game differently," Martin said. "We set out how we thought this team could win with the personnel we had and with the young quarterback. Most people say 'OK, you're going to play the young guy, you're playing for the future.' We just went 12-0 with the young guy and he got yanked four times.
"The rest of the world wants 12-0 with no warts. We have plenty of warts. Somehow we're 12-0. Just goes to show the job (Kelly) did that we made it work week in and week out with what we have."
Kelly's ability and willingness to adapt have been his greatest strengths.
"He made some of his biggest changes ever in the last year. Going away from some things that really were his bread and butter, and 12-0 later, the guy did it again," Martin said.
"He saw what Notre Dame football needed in 2012 and he got to know this university."