He played college football for the Stephen F. Austin Lumberjacks and was selected by the Philadelphia Eagles in the third round of the 1998 NFL draft.

Trotter is one of just four linebackers in Eagles history to earn four or more Pro Bowl invitations, joining Chuck Bednarik, Maxie Baughan, and Bill Bergey in that select group.

In his second season, newly hired Head Coach Andy Reid named Trotter the starting middle linebacker.

Trotter and the Eagles defense ranked second in the NFL in 2001, earning them their first NFC East championship since 1988.

He was designated with the franchise tag by the Eagles, but after failing to agree on a contract, became a free agent.

Trotter returned to the Eagles for the 2004 season, signing a one-year contract worth the veteran minimum.

That year, the Eagles advanced to their first Super Bowl since 1980, marking Trotter's first appearance in the championship game, though they would lose by a narrow margin to the defending champion New England Patriots, 24–21.

After officials reviewed video to see who instigated the fight, both Trotter and Mathis were ejected before kickoff.

The fight led to an NFL rules change where non-kickers cannot enter a neutral zone between the 45-yard-lines prior to the game.

[6] After Stewart Bradley tore his ACL during training camp, the Eagles needed an experienced middle linebacker to take his place for the season.