Kelly, who interviewed with the Philadelphia Eagles earlier in the week, says his interest with the NFL is over for now.
"Like every kid who has ever put on a pair of football cleats, I have had thoughts about being a part of the NFL. However, after much reflection and conversation with those closest to me, I have decided to remain at Notre Dame," Kelly said in a statement.
"This decision was motivated purely by my love for Notre Dame and the entire Fighting Irish community, the young men I have the great fortune to coach, and my desire to continue to build the best football program in the country."
The remarks were the first comments by Kelly since news broke late Wednesday that he had interviewed with the Eagles a day after the Irish were beaten 42-14 by Alabama in the BCS title game.
Notre Dame athletic director Jack Swarbrick said in a statement that he wasn't surprised by Kelly's decision.
"I was always confident that Brian would continue to lead our football program, I am very happy to have that confirmed and share Brian's excitement about what lies ahead for our program," he said.
Swarbrick, who also hadn't made any comments since the news broke, said he appreciated the Eagles and Kelly keeping him informed of what was going on throughout the process.
"We all look forward to what's ahead for Notre Dame football," he said.
Kelly led the Irish to a 12-1 record this past season and a No. 4 ranking, their best finish since they were No. 2 after the 1993 season, which is the last season the Irish won a major bowl game. The Irish haven't won a national championship since 1988.
The good news for the Irish is Kelly is expected to sign a top recruiting class next month and some recruiting analysts have said the Irish could nave the nation's No. 1 class.
"We still have a lot of work to do and my staff and I are excited about the challenges ahead," Kelly said.
The Eagles, who also interviewed Oregon coach Chip Kelly, said in a statement saying they spent a lot of time and effort looking at coaches they believed were the best collegiate candidates.
"We did so knowing that there was a remote chance that these coaches would leave their current posts. We understood that going into the process, but we wanted to leave no stone unturned while trying to find the best head coach for the Philadelphia Eagles," the statement said.
"We have no regrets about the effort we made in that direction and we will continue to proceed as planned in our search."
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