St. John's Prep is one of 13 secondary schools sponsored by the Xaverian Brothers in the United States. The brotherhood, founded in 1839 by Theodore James Ryken, is an international teaching order within the Roman Catholic Church.

Along with lay teachers, the brothers provide a Catholic high school education to 1,250 young men studying at the Prep from Massachusetts and New Hampshire. The school has graduated more than 13,000 students since 1907, offering a broad range of elective courses with core academic studies, 19 Advanced Placement courses, and numerous service opportunities, both locally and internationally. Each year, the school hosts the Walk for Hospice, which raises funds for North Shore Hospice.

A number of extracurricular activities are also available, including student productions in the black box theater at the Ryken Center for the Arts. The Eagles compete in 20 interscholastic sports—athletic fields encircle the campus—and 25 intramural sports. There are more than 6o student clubs.

The picturesque 175-acre campus, in addition to a retirement home and cemetery for the brothers, is also home to Camp Christopher in the summer, a weeklong camp for children ages 5 to 12, which is run separately from the school.