Koppen entered the 2003 NFL Draft following college and was selected by the New England Patriots in the fifth round with the 164th overall choice. Koppen entered the 2003 season as the backup to Pro Bowl center Damien Woody; however, Woody missed Week 2 with an injury, giving an opportunity for Koppen to start his first NFL game. Woody returned the next week, but a season-ending injury to starting guard Mike Compton allowed Woody to slide to the guard position and Koppen to start the remainder of the season at center, including the Patriots' Super Bowl XXXVIII win over the Carolina Panthers. Following the season, Woody signed with the Detroit Lions, leaving Koppen as the Patriots' starting center. Koppen started all 16 games for the Patriots in 2004, earning his second Super Bowl ring in as many seasons with the Patriots' victory over the Philadelphia Eagles in Super Bowl XXXIX.