On February 14, 1991, the Kansas City Comets selected Kelly in the third round of the Major Soccer League draft.
On September 11, 1998, the Heat traded Kelly to the Baltimore Blast in exchange for Michael Henning and cash.
In 2006, Kelly was hired as the head coach of the Baltimore Blast of the Major Indoor Soccer League.
He was named interim player-coach after his predecessor Tim Wittman was suspended by the league for assaulting a referee.
On 28 May 2020, the Blast announced that Kelly had "moved on" and that his assistant David Bascome would be taking over as head coach.