The team said in a written statement Kelly had earlier this month decided to remain at Oregon but changed his mind about the NFL opportunity and would become the Eagles' 21st head coach.
"Chip Kelly will be an outstanding head coach for the Eagles," team owner Jeffrey Lurie said in a statement. "He has a brilliant football mind. He motivates his team with his actions as well as his words. He will be a great leader for us and will bring a fresh, energetic approach to our team."
The Eagles have been looking for a shot in the arm after a disappointing 4-12 season that turned out to be the final one of Reid's 14-year tenure in Philadelphia. Known for its high-octane offense, the Ducks ran up a dazzling 46-7 record in four years under Kelly and averaged nearly 50 points per game.
Kelly's arrival raises the likelihood the highly mobile Michael Vick will remain the Eagles' starting quarterback.
Kelly, 49, interviewed with the Eagles in Arizona the day after Oregon played in the Fiesta Bowl. At the time, it was reported Kelly had decided to stay with the university. It was not clear what changed his mind in the 10 days after the Arizona meeting.