In 1994 he was appointed Publius Virgilius Rogers Professor of American History at Hamilton College.
In 2002, Paquette protested when a student group invited Annie Sprinkle, an actress and former porn-star, to speak on campus.
[4] Paquette later led an attempt to create an alumni-endowed center on campus dedicated to "the study of capitalism, natural law and the role of religion in politics," but the initiative was ultimately rejected by the faculty and administration.
[5] In response, Paquette co-founded the independent Alexander Hamilton Institute for the Study of Western Civilization, housed off-campus in the nearby village of Clinton.
In response to the College's handling of the Institute issue and other matters, Paquette formally resigned his endowed professorship (though not his faculty position) in 2011.