[6] St. Francis is run by the Franciscan Brothers of Brooklyn, who maintain a residence on the top floor of the school.

[2] St. Francis Preparatory originated as St. Francis Academy, a small all-boys high school on 300 Baltic Street in Brooklyn, New York, founded by the Franciscans Brothers of Brooklyn (O.S.F.).

[citation needed] There are currently plans to add a three-story addition to the rear of the existing building.

[8] St. Francis Prep has a rivalry with Holy Cross High School, fueled particularly by their football teams.

Known as the "Battle of the Boulevard" due to the two schools being located only 2 miles apart on Francis Lewis Boulevard,[9] the rivalry between the Prep Terriers and the Holy Cross Knights has been called "arguably the greatest rivalry in New York City football.