He signed with the Arena Football League's Orlando Predators in 2004 and guided the team to a 9-5 record and the playoffs, despite suffering another knee injury and missing two and a half games.
He was then signed by the Indianapolis Colts in 2004, reuniting with former Buccaneers coach Tony Dungy, but only saw limited action in one game before being released during the season.
He returned to the Orlando Predators where he was the starting quarterback through the 2006 season. He has a 32-15 record as the Predators' starter and led them to ArenaBowl XX in 2006, losing 69-61 to the Chicago Rush. With a win, Hamilton would have become the first player in history to own both a Super Bowl and ArenaBowl ring. In the 2006 off-season, he was released by the Orlando Predators and has yet to sign with another team or officially announce his retirement.
He returned to school, and received his degree in History, Technology, and Society in August 2007. "
In 2008, following an arrest for a hit and run, DUI, open container and marijuana possession, Joe Hamilton resigned as a Georgia Tech assistant coach—less than two weeks after he was hired.
In 2010, he resurrected his coaching career when he became a recruiting intern at Georgia State, which had launched its Georgia State Panthers football team that year. In June 2011, he joined the Panthers' full-time staff as running backs coach. On May 7, 2013, exactly 5 years after submitting his resignation, Hamilton was re-hired by Georgia Tech to provide assistance with recruiting for the Yellow Jackets football team.
1998 - One ACC Offensive Back of the Week Award, 1st Team All-ACC Quarterback, Co-MVP of 1999 Gator Bowl against Notre Dame, led the team to ending 7 year losing streak to the Georgia
1999 - Davey O'Brien Award winner, Runner-up to the 1999 Heisman Trophy, 1st Team All-America Quarterback, 1st Team All-ACC Quarterback, Three ACC Offensive Back of the Week Awards, defeated University of Georgia 51-48 for second straight year in wild overtime victory