Kelly was drafted 94th overall by the Ottawa Senators in the 1999 NHL Entry Draft. He spent one year in the American Hockey League (AHL) with the Grand Rapids Griffins and three seasons in the same league with the Binghamton Senators. He also played with the Muskegon Fury (of the UHL) for four games (recovering from an injury). In 2004–05, he had finished fifth in the AHL in plus-minus with +30. He also finished fifth on Binghamton with 60 points, as the team finished fourth overall in the League. When he was a professional rookie in 2001–02, he helped the Griffins finish fourth in the AHL. In his two final seasons in Binghamton, Kelly served as team captain.