Hamill was recruited late in the 1994 AFL Draft, with the 79th overall pick. Making his senior debut in 1996 with the Carlton Blues, Hamill was a favourite among supporters for his strong marking and goalkicking. He was a key part of the Blues 1997 pre-season premiership side and was also part of Carlton's runner up team in 1999. He played with Carlton from 1996 to 2000 with 92 games and 114 goals. At the end of the 2000 season he was traded to St Kilda, after having an argument with Carlton president John Elliott.
At the end of 2000 he moved to St Kilda, among other big name signings, such as Fraser Gehrig and Steven Lawrence. He was named captain of the Saints for the 2003 season and his influence for the team was unquestionable. He had a tough, uncompromising style, always committing himself to the contest. As a result, he sustained many injuries over his career, and midway through 2005 he missed a large part of the season with an assortment of hip, shoulder, and knee injuries. Due to the same array of injuries, he missed the entire 2007 season. Doctors advised Hamill that he should retire from the game due to the toll it takes on his body. Although he had the desire to continue, many coaches and medicos told him he was unable to continue. After seeking a trade mid season, he decided to retire, closing the book on an illustrious career at both Carlton and St. Kilda.
Retirement
On 3 October 2007 Hamill announced his retirement from AFL football. Hamill played 190 AFL matches with Carlton and St Kilda. In a career crippled by injury towards the end, he was remembered for his uncompromising attack on the football. He was a member of preseason premiership sides at both clubs. "The decision to retire has been one of the hardest to make in my football career. However, I felt it was in the best interest of the club moving forward", Hamill said. "This will now allow a younger player to step up and cement themselves in the St Kilda side... I would like to thank my family and close friends for their support over the journey. I am grateful to the Carlton Football Club for providing me with the opportunity to play and develop as a footballer", he said. "Their inspirational leaders taught me to crave success and dedication to a cause, which will stay with me forever. I would also like to express my gratitude to Grant Thomas whose efforts did not go unnoticed by the playing group during his six years as coach. I wish Ross Lyon and the St Kilda Football Club all the best moving forward and hope that the current playing group will achieve the ultimate success." St Kilda coach Ross Lyon reflected on Hamill's contribution to the club. "Aaron is a tremendously respected figure and he has played a significant role in getting this team to where it stands today. We all wish him the best in his retirement as he prepares for life after footy."