Kelly joined the Grand Valley State University staff in 1987 as a graduate assistant and defensive backs coach for Tom Beck and became the defensive coordinator and recruiting coordinator in 1989. Kelly took over as head coach in 1991. In his final three seasons the Lakers went 41–2, at one point winning 20 consecutive games. The Lakers went 14–0 in 2002 en route to their first national title and went 14–1 in 2003 when they claimed their second National Championship. Kelly was named the AFCA Division II Coach of the Year after each of these championship years.