The Woodridge College and Preparatory School on the outskirts of Gqeberha announced the death of one of their Grade 12 pupils, expressing their deepest sadness in a statement issued on Friday.
The school's head of Marketing and Communication Lynne Niemann says Troy Schofield died following a short illness.
She says he was admitted to hospital on Tuesday and passed away on Thursday.
Niemann says Troy joined Woodridge as a boarder in Grade 10 and was a fantastic sportsman and gifted athlete who won several races at school.
She says the entire school community is devastated by Troy's death and he will be deeply missed by teachers, coaches, staff and fellow pupils.
The school is offering counseling services for any pupils or staff who need support in coping with the loss.
"This is an extremely difficult time for our school community. We ask that everyone's privacy, especially that of the Schofield family, be respected as we all grieve this tragic loss together," said College Headmaster, Luke Hartley.
A prayer service paying tribute to Troy will be held at school on Friday.
The College will also close three days earlier than the anticipated end of term.
In May this year, a Grade 5 learner from Clarendon Park Primary School in Gqeberha also died after a short illness.