He just needed more time to make the decision.
"The hardest thing for me to do was to leave Oregon," Kelly said Thursday at a news conference introducing him as the 21st coach in team history. "I knew it was a great fit, but it was whether I could leave what I have. I love those guys and it had to be a special place for me to leave."
The Eagles hired Kelly on Wednesday, giving him a five-year contract and ending an exhaustive search to replace Andy Reid. The offensive innovator was lured away from Oregon, where he went 46-7 in four seasons and turned the program into a national powerhouse.
From the start, Kelly appeared to be Philadelphia's top choice. But two days after a nine-hour meeting in Arizona with owner Jeffrey Lurie, general manager Howie Roseman and president Don Smolenski, Kelly chose to stay at Oregon.
The Eagles continued interviewing other candidates, and were close to offering the job to Seahawks defensive coordinator Gus Bradley on Tuesday night. But Kelly changed his mind after thinking harder about making the move and talking to several people, including Reid who quickly moved on to become Kansas City's coach.
"I knew this was the best spot, but there's so much more to it," Kelly said. "What happens when I leave? Who becomes the next head coach? What happens to those players? You're not making reservations for dinner. You are changing not only your life, but a lot of other people's lives."
Kelly said he became emotional when he told players in a meeting that he was leaving, and added that he cried more than they did.
He went from a warm and fuzzy environment in Eugene, Ore. to a hero's welcome in the city of Brotherly Love.
Fans greeted him at the airport when his plane arrived in Philadelphia on Wednesday night and a sign reading "Our Chip's Come In" was hung on two trees outside the team's practice facility on Thursday morning. A few fans drove down Pattison Avenue honking their horns to salute the hiring.
"It's a really exciting time for me. It was a difficult decision. There's not many opportunities to coach in the National Football League, and every one of them is special," Kelly said. "But this is an iconic franchise with an outstanding owner. I knew what this place was all about, and this is where I wanted to be. It was just a matter of figuring out how to do it the right way."
The Eagles interviewed 11 candidates in slightly more than two weeks. While fans became anxious waiting for a new coach, the team emphasized a patient approach.
Perhaps they were waiting for Kelly to reconsider.
"The key was to find the right leader, not make the fastest decision," Lurie said. "We never took 'No' as a full 'No.' We knew he was torn. And we knew there was no competition for Chip. It was just, did he want to stay or did he want to come to us?"
Though Kelly has no previous NFL experience, the Eagles are banking on him to turn around a franchise that has just 12 wins in the last two years and zero playoff victories since 2008.
"Chip is a trendsetter," Roseman said. "People are following him. He's not a disciple of anyone. When you are trying to find greatness, you have to find the people on top."
Kelly built quite a reputation for being one of the sharpest football minds in college while leading Oregon to four straight BCS bowl games - including a bid for the national championship against Auburn two seasons ago - and three conference championships.
Some aspects of his hurry-up, spread offense are used by New England and Washington. Patriots coach Bill Belichick even brought Kelly in to get advice on his offensive philosophy.
But Kelly has a challenge in Philadelphia. His flash-and-dash offense needs a leader under center. Nick Foles, a third-round pick last year who replaced Michael Vick, is a dropback quarterback who said himself that he doesn't fit Kelly's zone-read style
Vick, who will be 33 when the season starts, isn't coming back for the $16 million he's scheduled to make next year. The Eagles have to make a decision on giving him a roster bonus of $3 million within three days after the Super Bowl.
"I haven't watched even film to make any decision on anybody," Kelly said, adding that he's a "huge fan" of Foles.
Kelly also talked about adapting his system to fit the players on the team, a quality that impressed Roseman in their first interview.
"When you meet with Chip, you realize very quickly that Chip is not about whether his offense is going to translate to the NFL," Roseman said. "It's about his vision for a program, it's about how he sees the entire aspect of a football organization and Jeffrey outlined in that first press conference: I want a leader, I want a presence, and so if you had any doubt about Chip Kelly's offense, you left and said this isn't about Chip Kelly and the spread, this is about how Chip Kelly approaches football, and that was incredibly, incredibly impressive."
The Eagles were 3-1 this season after a 19-17 win over the New York Giants on Sept. 30. They then lost 11 of their last 12 games to finish in last place in the NFC East. Reid was fired the day after the season ended, ending a 14-year tenure in which he won more games than any coach in franchise history and went to the playoffs nine times, including five conference championship games.
But the Eagles are still seeking their first Vince Lombardi Trophy and first NFL title since 1960.
"We have one goal, and that's to get to the Super Bowl," Kelly said. "It's not an 'I' deal, it's a 'we' deal. Our players will understand that."