This school named after the Jesuit missionary, Jean de Brebeuf, opened with one hundred Grades 9 & 10 students in September 1963. Their Excellencies, Bishops Philip F. Pocock and Francis A. Marrocco presided at the official opening and solemn blessings on January 5, 1964. Brebeuf's first graduating class in 1966 consisted of 30 students, among them Mr Michael Daoust formerly the head of mathematics at Brebeuf. The 1967 year had 74 graduates, one of whom was Mr Robert Lato, former head of guidance at Brebeuf.

In 2001 the Toronto Catholic District School Board announced funding for a new building to replace Brebeuf's outdated facilities invested in $23 million. The main architect was Rod Robbie and Kneider Architects. Under Principal Michael Pautler '76, the Brebeuf community was temporarily housed in the former Bathurst Heights Secondary School (later John Polanyi Collegiate Institute) while the new building was being constructed. On January 5, 2004, exactly forty years after Bishop Pocock presided over Brebeuf College School's Solemn Blessing, staff and students began classes in the new facility at the old campus. It was blessed in April of that year.

• - Kneider Architects
• - Robbie Sane Architects