Hendrik Kanise was established in 1925 as a multi-racial church school. Back then it was called Wesleyan Native Day School which had only 4 teachers, including the principal Mr, Masoka, and classes from Sub A to Standard 4. Mr Masoka was then transferred to bigger schools because of his good job running the school. Then in 1927, the school got a new principal Mr. W. Mbethe, and because the learners were increasing in numbers, the teachers were also increased and the classes went from Sub A to Standard 6.

In 1933, the Department of Education decided that the school needed to be divided into two schools where we had black school and coloured school separately, and that is when the school had a new name, Jolisa Phezulu. After a couple of years, the school committee then decided that the school needed to change the name, and it was named after the committee chairperson Mr. Hendrik Kanise.

In 1969, the school got new buildings in Nonzwakazi Location, where it is still standing. The new school had 6 classes and one office with a new principal, Mr. Mzileni, with 13 Teachers, then the school went from Sub A to Standard 7. In 1984, they got a new principal Mr. V.M. Nqini, and 3 years down the line changed to Mr. Mbatha. In 1991, the school got a new principal, Mr. Kosi, who worked very hard in making sure that the school does not only get new buildings but it goes up to Standard 10. The plea was accepted and that was when the school became a combined school. Sadly, Mr. Kosi pass away in 2004, then Mrs. Louw-Balie became the first woman to be a principal at the school and she remained the principal until she retired at the beginning of 2017.