The aim of starting Khanyisa High School by Mr.S.M. Vattakunnel 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 are 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 school related matters.