Since its founding, Monsignor Bonner has been run by the Order of Saint Augustine of the Province of St. Thomas of Villanova. It is one of nine  Augustinian high schools in North America. Bonner has a storied history with the Augustinians, as those assigned to Bonner reside in the friary behind the school. Bonner is also renowned for retaining alumni as faculty and administration, a great testament to the Bonner tradition and the strong sense of community that embodies the school. Currently, there are 22 alumni on staff, including the former president, Rev. Augustine M. Esposito, O.S.A., Ph. D., '69. In September 2005, it was announced that the Office of Catholic Education of the Archdiocese of Philadelphia was implementing an administrative restructuring of Monsignor Bonner High School for Boys and the neighboring Archbishop Prendergast High School for Girls. Essentially, the schools would begin operating under one administration beginning on 1st, July, 2006. Bonner's president was appointed president of the new co-institutional Monsignor Bonner & Archbishop Prendergast Catholic High School. The Principal of neighboring Archbishop Prendergast High School, Mrs. Mary Berner, was named Principal of the co-institutional school in January 2006.
The Augustinian Friars left campus and removed themselves from the day-to-day activities of the school at the end of the 2008-2009 academic school year. Due to the lack of priests in the Augustinian Order and the expense to the Province of Saint Thomas of Villanova, they decided to leave and focus on the remaining parishes, ministries, facilities, and educational institutions in which they serve. Many of Bonner's friars relocated to nearby Malvern Preparatory School.
The position of President established in 1993 for all Archdiocesan High Schools. The President is responsible for financial operations, facilities issues, fundraising, alumni relations, and external affairs.
1993 to 1996: Rev. Gordon Marcellus, O.S.A.
1996 to 1999: Mr. Thomas Smith
1999 to 2001: Rev. John Denny, O.S.A. '75
2001 to 2009: Rev. Augustine M. Esposito, O.S.A '69
The Principal was originally the top administrator in the school. In 1993, this shifted when the Presidency was introduced. Since then, the Principal has handled the day-to-day operation of the school.
1953 to 1959: Rev. John Gallagher, O.S.A.
1959 to 1962: Rev. Kenneth Kennedy, O.S.A.
1962 to 1967: Rev. Thomas Mahoney, O.S.A.
1967 to 1972: Rev. David Duffy, O.S.A.
1972 to 1974: Rev. Francis Sevick, O.S.A.
1974 to 1976: Rev. Harry Erdlen, O.S.A.
1976 to 1979: Rev. George Burnell, O.S.A.
1979 to 1987: Rev. Francis Horn, O.S.A., '67
1987 to 1993: Rev. Gordon Marcellus, O.S.A.
1993 to 1999: Rev. John T. Denny, O.S.A., '75
1999 to 2005: Dr. Thomas F. Rooney, EdD, '62
2005 to 2006: Mr. William Brannick, '95 (Acting Principal)
2006 to 2007: Mrs. Mary Haley Berner, (first co-institutional Principal)
2007 to present: Mr. William E. Brannick, '95 (co-institutional Principal)
This article's list of alumni may not follow Wikipedia's verifiability or notability policies. Please improve this article by removing names that do not have independent reliable sources cited within this article showing they are notable and alumni or by incorporating the relevant publications into the body of the article through appropriate citations.(October 2015)