It played its first season in Division I in 2000, also hiring head coach Jon Mueller that year. After competing as an independent in 2000 and in the New York State Baseball Conference in 2001, it played its first season in the America East in 2002. In 2004, the Great Danes set a program record with 37 wins and reached their first Division I postseason, going 1–2 at that season’s America East tournament.