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, and which was the last team for which he actively appeared as a player. 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).