Brought Manhattan College Athletics to a new level during his tenure as the College's President, creating a program that was balanced for both men and women with scholarships available for all 19 Division I athletic teams on campus. Brother Scanlan was instrumental in bringing three new programs to campus-women's soccer, men's lacrosse and women's lacrosse. With 72 MAAC Post-Season Championships and 18 MAAC Regular-Season Championships notched on his belt, Brother Scanlan ensured academics were not compromised while enhancing the athletic program. Hundreds of All-Academic MAAC athletes attest to the integrity of an athletic program that proved excellent students could also excel on the court and field.

During his tenure, the men's basketball team reached the NCAA Tournament for the first time in decades and reached the Round of 32 twice with victories over Oklahoma in 1995 and Florida in 2004. In 1995, it became the only MAAC basketball program in league's history to have received an at-large bid to the NCAA Tournament.

Facilities were also enhanced under Brother Scanlan's leadership, including the addition of a state-of-the-art multipurpose turf facility at Gaelic Park.  Gaelic Park now serves as the home to Manhattan soccer, lacrosse and softball, as well as the college's intramural programs.