With Ricky Williams suspended for the entire season, Brown entered 2006 as the feature back for the Miami Dolphins. The offensive line and offense in general struggled for the Dolphins, making it difficult for Brown to consistently produce at a high level. He had a breakout game on October 15 loss to the New York Jets, rushing for 127 yards and a touchdown on 22 carries. Three weeks later he rushed for a career-high 157 yards against a stingy Chicago Bears defense, helping the Dolphins to an upset victory of the previously undefeated Bears. On a Thanksgiving Day game against the Detroit Lions, Brown suffered a broken left hand from a hit by a defender's helmet. While he missed the next three contests, Brown returned for the final two games of the season and posted back-to-back 100-yard rushing performances against the Indianapolis Colts and New York Jets. In 13 games played, Brown finished with 1,008 rushing yards, 276 receiving yards, five touchdowns and a solid 4.2 average.