Kelly's predominant professional football career was as an Arena Football League quarterback playing some of his career with the New Orleans VooDoo, for whom he played for in 2005 and 2007. He previously played for the Charlotte Rage (1993, 1995–96), Nashville Kats (1997–2001), Dallas Desperados (2002), Detroit Fury (2003–2004), Kansas City Brigade (2006) and Utah Blaze (2006). At the end of the 2006 season, he held several all-time AFL career records, including touchdown passes (767), passing yards (39,948), pass attempts (5,827), pass completions (3,621), and interceptions (155).
On December 6, 2007, Kelly was named the head coach of the proposed new All American Football League's Tennessee team. The league suspended operations March 12, 2008 (permanently, as things later developed, although only a delay was announced at the time), and Kelly signed with the Georgia Force two weeks later on March 26, 2008, but never participated as an active player for the Force. Kelly retired as an Arena Football player following the 2008 season and currently serves as a commentator on Tennessee Volunteers football radio broadcasts.
In June 2013, Kelly was nominated for the AFL Hall of Fame.