Eagles Coach Chip Kelly watched Barkley for four years while coaching at Oregon. Barkley, the 98th overall selection, was the fourth quarterback chosen.
The Buffalo Bills chose Florida State's EJ Manuel with the 16th pick in the first round, the New York Jets selected West Virginia's Geno Smith in the second round and the Tampa Bay Buccaneers took North Carolina State's Mike Glennon in the third round.
Barkley, a four-year starter, passed up the opporunity to turn pro after the 2011 season and returned for a final year with the Trojans.
He finished his career as the school's all-time leader in numerous categories, but his Heisman Trophy hopes faded last fall as the Trojans spiraled from preseason No. 1 to a 7-6 record. Barkley passed for 36 touchdowns, with 15 interceptions, in 11 games.
He was sidelined against Notre Dame and for the Sun Bowl against Georgia Tech after sustaining a shoulder injury against UCLA.