Green made his AFL debut in 2000. Melbourne had a highly successful year in 2000 and in his first year of AFL football Green played an important role in the Melbourne forward line. Melbourne made the Grand Final, but were ultimately unsuccessful, losing to Essendon.
After working his way into a greater role in the midfield in 2004, Green found plenty of the ball both forward and through the midfield in 2005. His penetrating and very accurate left foot kicking was effective to leading forwards or in front of goals. He often sets up Melbourne's marking forwards. He played in 21 of a possible 23 games in 2005, consolidating himself as an integral part of the Demons outfit in 2006 with consistent displays in the midfield and excelling as part of the leadership group. Green wears the number 18 guernsey for Melbourne.
Described, as a "soft" player early in his career, Green became renowned for his acts of courage mid-career, attacking the football with vigour and courage. This resulted in him taking a higher number of contested marks in 2007. In the 2007 season, he played very good football both in defence, the midfield, and in the forward line. Green continued his solid form into the 2008 season, being one of Melbourne's few highlights in a miserable season. It took time for Green to decide if he wanted to go on and play with the Demons in 2009 but eventually signed a contract and agreeing to stay red and blue for another three years.
In 2010, Green had his best season to date, kicking 55 goals and taking 153 marks, both ranked sixth in the AFL, in a young Melbourne side to make the All-Australian squad and win his first Keith 'Bluey' Truscott Medal. Green finished on 295 votes to win the award from James Frawley (277) and Mark Jamar (231). He also won the Ron Barrassi Leadership Award and the "Heart and Soul" Award, pushing his case to be the next captain of the Demons, after the retirement of James McDonald.
The 2011 season started successfully for Green as he was named the new Melbourne captain in late January. Succeeding James McDonald, who retired at the end of 2010, Green described being named captain as a "surreal experience". After a relatively successful first year as captain of the club, Green was named captain of the Australian International rules football team for the 2011 Series in Australia. Green was the only Australian to kick a goal during the 2011 International Rules Series, many commentators named this goal a 'captain's goal'.
Before the 2012 season, under new coach Mark Neeld, Green was removed from the captaincy and the leadership group altogether in favour of a new and younger group of whom only two were retained from the previous year.
Green played his 250th AFL game in Round 18 against North Melbourne, coincidentally the same team against whom he made his AFL debut back in 2000. On 8 August 2012, Green announced that he would retire at the conclusion of the 2012 season.