In September 1914, 110 students started classes in Cathedral College's temporary quarters at Saint John’s Chapel in the Fort Greene section of Brooklyn.

Upon completion of the six-year program, students continuing on to priesthood would be assigned to a major seminary.

[5] In 2002, the rector of Cathedral Prep, Monsignor Charles M. Kavanagh, was accused of sexual abuse by a former seminarian at the school.

The accuser, Daniel Donahue of Portland, Oregon claimed Kavanagh had made unwanted advances and touched him inappropriately in the 1980s, starting as an eighth grader at the seminary and continuing at Cathedral College.

Since 1968, each summer Cathedral has hosted the Father Edward W. Troike Leadership Program for young men of 6th and 7th grades, as well as incoming freshmen.