In 2009, Kelly was the head coach and general manager for the Winnipeg Blue Bombers of the Canadian Football League (CFL).
Kelly was the offensive play-caller with the Winnipeg Blue Bombers between 1992 and 1996, as part of the teams that captured three regular season division titles and appeared in the Grey Cup twice.
Kelly was fired nine games into the 1999 season and replaced by assistant Mark Nelson, who was appointed interim head coach.
Kelly's offence led the league in red zone scoring percentage, with quarterback Jeff Brohm named First-Team All-XFL.
Kelly spent five years in the National Football League (NFL) working as an advanced pro scout for the Washington Redskins and Philadelphia Eagles where he also was an offensive assistant/quality control.
[5] Kelly also coordinated the offense for half of the season, in which the team went 7–11 missing a home playoff berth by a single game.
Ken Hildahl, chairman of the Blue Bombers, indicated that Kelly's dismissal was due to the performance of the team, not the incident earlier that day.
[11] In 2017, Kelly was named the East Coast Football Officials Association (ECFOA) Division III Coach of the Year.