On October 17, 2006, McFarland was traded to the Indianapolis Colts for a second-round pick in the 2007 NFL Draft. The trade reunited him with Tony Dungy, his head coach in Tampa Bay during his first three seasons. At the time of the trade, the Colts ranked last in the league in run defense, allowing over 116 yards per-game, and had lost defensive tackle Corey Simon to a season-ending injury the week before. McFarland made his first sack as a member of the Colts against the Buffalo Bills on November 10. He finished the regular season with 33 tackles and 2.5 sacks, although the Colts finished last in rush defense. In the playoffs, the Colts defense became stifling, limiting the Kansas City Chiefs to 44 rushing yards, the Baltimore Ravens to 83 and the New England Patriots to 93. McFarland started in Super Bowl XLI and recorded a sack, as the Colts defeated the Chicago Bears, 29–17, capturing his second Super Bowl ring.
