In 1993, Farrell was appointed Executive Assistant to the president of St Patrick's, a new position. He was appointed Vice-President in 1996 and following the sudden death of Matthew O'Donnell in 1996 was appointed President of St Patrick's College and the National Seminary. He remained president of St. Patrick's when it was separated from the seminary by the Universities Act 1997. Farrell presided over the revision of the formation programme "Pastores Dabo Vobis" at St Patrick's. He also supervised the renovation of its heritage buildings.