Kelly was interviewed for the Eagles' vacant head coaching job only hours after the Fighting Irish fell to Alabama in Monday's BCS National Championship Game, raising the possibility he could be leaving the school.
But Kelly issued a statement Saturday announcing he has chosen not to jump to the professional football ranks.
"This week, I had an incredible opportunity to speak with one of the premier organizations in sports about becoming their head coach," Kelly's statement read.
"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 this year guided the Irish to an undefeated regular season, becoming just the second coach in team history compile 12 wins in a single season.