During the period from 1932 to 1962 classes for the school were held in part of the building that now, and then, housed the grammar school and church. On June 12, 1960 ground was broken for a new high school building and the dedication ceremony for the new high school took place on May 20, 1962. The new school building opened in September of 1962 and graduated its first class of two hundred and thirty two graduates in June of 1964.
In September of 1994 the school was again re-named as St. Edmund Preparatory High School and became an independent entity run by a Board of Trustees. At this time, the school became a co-educational institution dedicated to preparing boys and girls for entrance to college. Bishop Thomas V. Daily approved the change after consultation with Monsignor Vincent D. Breen, Superintendent of Catholic Education, and Monsignor Thomas F. Noonan, pastor of St. Edmund Church. The proposal to enroll boys was made to the Bishop in response to an increasing number of inquiries in recent years from parents who sought a Catholic High School to serve boys from parishes in South Brooklyn.
From its opening in 1932 the administration of the school was in the very capable hands of the Dominican Sisters of the Congregation of Our Lady of the Rosary of Sparkill, New York. However, in 1986, as the number of Dominican teaching faculty decreased, the administration of the school was turned over to the equally capable hands of the Congregation of The Sisters of Saint Joseph. In 1995 Mr. John Lorenzetti was named as the first lay principal of St. Edmund's and was assisted by Sr. Barbara Doyle C.S.J. as Assistant Principal.
In September of 1999 Sister Barbara was appointed Campus Minister and Mr. James Benson was appointed as the first lay Assistant Principal. Due to the ever increasing student population it was determined that another layer of administration was required and Mr. Tom Maher and Mr. Ray Malafronte were appointed Academic Deans. In September of 2005, Mrs. Allison McGinnis was appointed as the school's second lay Assistant Principal. In September of 2008, Mr. Kevin Raphael was appointed as the school's third lay Assistant Principal.
On February 14, 2007, St. Edmund Prep took the first step towards expanding our physical school building with a Groundbreaking Ceremony for the new Library & Media Center Wing. Bishop Nicholas DiMarzio presided over the ceremony. January 31, 2008 saw the final piece of steel rise into place, completing the building's basic shell. A Topping Off Ceremony was held, where members of the St. Edmund Community signed the beam that would be hoisted into place. Auxiliary Bishop Frank Caggiano presided over the ceremony. The new wing was officially dedicated on the Feast of St. Edmund of Canterbury, November 16, 2008. Bishop Nicholas DiMarzio presided over the Mass of Thanksgiving and Dedication Ceremony.
Responding to the needs of our students, St. Edmund Prep cemented our place as an institution dedicated to rigorous academic study when the school officially became an International Baccalaureate World School in September 2008 an began teaching IB courses in the Fall of 2009.
In June 2014, Rev. Edward Brophy retired as Pastor of St. Edmund Parish and ended his tenure as Chairman of the Board of Trustees, a post he held since coming to St. Edmund Parish in 2001. On June 30, 2014, Rev. David Dettmer became the Pastor of St. Edmund Parish and assumed the role of Chairman of the Board of Trustees.
On March 8, 2017, after twenty-two years as the Principal of St. Edmund Prep and forty-eight years in Catholic education, Mr. John Lorenzetti informed the Board of Trustees of his plans to retire at the end of the 2016-2017 school year. On May 4, 2017, Rev. David Dettmer, Chairman of the Board of Trustees announced to the school community that Mrs. Allison McGinnis would serve as the eleventh principal of St. Edmund Prep, beginning at the start of the 2017-2018 academic year. Ms. Peggy McEvoy would serve as the 4th lay Assistant Principal in September 2017.