Khanyisa High School was started by the Catholic Church in 1994. The aim of starting this school was to provide quality education, based on sound Christian values, to children in and around Mthatha. By providing Christian Education the school assists the development of the whole person of the child in an environment in which all members of the school community is challenged to live out the Gospel values in the context of our rapidly transforming society. The school is managed by a Board of Directors drawn from the Diocese of Mthatha and the School Governing Body. The School Governing Body comprises of representatives of parents, educators and learners. The school governing body is answerable to the Board of Directors which in turn is answerable to the Diocese of Mthatha concerning all administrative and financial matters of the school.