Kelly was a four-year defensive standout for the Pioneers men's lacrosse team from 1997 through 2000. In his final three seasons he helped lead C.W. Post (now LIU Post)  to the National Championship game and earned numerous honors along the way. All four years of his career, Kelly was a NYCAC All-Conference First Team and earned the conference's Rookie of the Year honor in 1997 and Player of the Year from 1998 through 2000. He was also a United States Intercollegiate Lacrosse Association (USILA) All-America First Team selection four straight seasons and a three-time recipient of the Division II Will C. Schmeisser Award, given annually to the country's top-defensive player. In addition, in 1999 and 2000 he was selected as the Lt. Raymond J. Enners Division II National Player of the Year Award winner.