He became Archbishop of Halifax on September 14, 1998. The Archbishop of Halifax is in charge of dioceses in the provinces of Nova Scotia and Prince Edward Island. Prendergast also became the Chancellor of Saint Mary's University in Halifax. This is because the university always had the archbishop as its chancellor. In 2007 the archdiocese and the university decided that the Archbishop would not be the chancellor anymore. Instead, he would be called the "Visitor" to the university.