While president of LMU, Loughran directed considerable financial resources to academics and lowered the minimum course load for professors from four to three, freeing up faculty for research and other scholarly and creative pursuits. He established classes in the study of American cultures, in part to raise awareness of the school's minority students who were pushing for greater recognition. He was president in 1990 when one of Loyola Marymount's top basketball players, Hank Gathers, collapsed during a game and died. Gathers' family brought a wrongful-death suit against Loyola Marymount that the school settled for $545,000. Loughran raised the university's endowment from about $21 million to $106 million before he resigned unexpectedly in 1991.
In February 1990, Loughran denied university recognition to a fledgling gay and lesbian student organization, the Alliance of Gays and Lesbians - Loyola Marymount University (AGL-LMU), despite the group's support from both the student and faculty senates and in disregard of the fact that its charter did not violate Catholic teachings. At the time of Loughran's decision, there was already a formally recognized gay and lesbian student group at Loyola Law School, which is part of Loyola Marymount University, though on a separate campus. Loughran's actions set off a contentious debate among students, faculty and staff. The organization struggled after its founding president graduated, though it survives in some form as of 2011.
In addition to his leadership positions at LMU and St Peter's, Loughran served as acting president of Brooklyn College in 1992, interim president of Mount St. Mary's College in Emmittsburg, Maryland, from 1993–94 and dean of Fordham College in New York. Fr. Loughran was an Associate Professor of Philosophy at Fordham from 1974–1984 and held the Edmund Miller, S.J., Philosophy Professorship at John Carroll University in Cleveland, Ohio from 1992-1993. Prior to returning to Saint Peter's as President, Loughran was Interim Vice President for Academic Affairs and Interim Dean of the Arts and Sciences faculty at Fordham.