Slightly over 10 months after his season-ending injury, Harrison returned to Patriots' practice for the first time on August 7, 2006. After sporadic playing time in the preseason, Harrison started the first seven of the Patriots' games in 2006, totaling 23 tackles and one sack. However, while making a tackle on Marvin Harrison against the Colts on November 5, Rodney Harrison injured his right shoulder and missed the next six weeks of the season. He returned to the Patriots in week 16, but his season was ended the following week in Tennessee after a low block from Bobby Wade injured his right knee.