The Department of Education wants 40percent of schools to be fee-exempt from next year.
Department of Education spokesman Lunga Ngqengelele said the funds would vary from province to province, depending on the levels of poverty.
Gauteng's Department of Education said 397 schools in the province were set to benefit next year.
Rebonwe Primary School, Ivory Park Secondary School and Altmont Technical High School in Soweto are among the schools that will be included.
Godfrey Maduna, the deputy principal of Ivory Park Secondary, said their school had to accommodate about 1800 pupils, who were expected to pay R80 each in yearly school fees.
"The fee exemption is not necessarily good news for us as we usually find that department funds are not enough - and the pupils' fees augmented the needs of the school."
Jon Lewis, media officer for the South African Democratic Teachers Union, said the news was welcome and hopefully a first step towards free education in all South African schools.