In 2005, the decision was made by the Office of Catholic Education of the Archdiocese of Philadelphia that Monsignor Bonner High School and Archbishop Prendergast High School would be a co-institutional model with one administration. The new administration would include a single President, Principal and Assistant Principals for Academic Affairs, Student Services, and Student Affairs for both schools. The new model became official in July 2006, with Bonner's President Rev. Augustine Esposito, O.S.A and Prendie's Principal Mrs. Mary Berner, as the President and Principal of the new Monsignor Bonner and Archbishop Prendergast Catholic High School. In 2007, Mr. William Brannick replaced Mrs. Berner as the principal of the co-institutional school. Two years later, in June 2009, it was announced that the Augustinian Friars, who were part of Monsignor Bonner since the creation of the school, would be leaving the school due to a low number of
priests. Father James Olson soon became the school's new president. The school faced a difficult time in January 2012 when Archbishop
Charles J. Chaput announced that Bonner and Prendie would close in June, due to the recommendations of the Blue Ribbon Commission. The basis of the commission's recommendation was founded upon the real estate value of the campuses and their potential income after possible retail development. Soon after the announcement was made, the Administration began the appeal process which outlined plans for the improvement of Bonner and Prendie. With the support of students, faculty, parents, and Alumni, money was raised to support the schools. In a 13-day span, alumni and supporters donated $1.11 million to keep the school open. Days before the final decision regarding the school was to be made, a group of business people came forward to help not just Bonner and Prendie, but the other high schools destined to close as well. On February 24, 2012, Archbishop Chaput announced that Bonner and Prendie would remain open as one combined school. The school is still represented by Bonner's mascot, the Friar and Prendie's mascot, the Panda. Homerooms remain single sex as do Theology classes and gym/health classes. == Shooting threat==