| SOA-5 | University of Western Cape | Cape Town | SOUTH AFRICA | AFRO | WHO Collaborating Centre for Oral Health | VARENNE Benoit | Active | Details |
| SOA-8 | North-West University (Potchefstroom Campus) | Potchefstroom | SOUTH AFRICA | AFRO | WHO Collaborating Centre for the Quality Assurance of Medicines | DESTA Abayneh Tamir | Active | Details |
| SOA-10 | University of Cape Town Medical School | Cape Town | SOUTH AFRICA | AFRO | WHO Collaborating Centre for Medicines Information | RAGO Lembit | Pending | Details |
| SOA-13 | University of Natal | Durban | SOUTH AFRICA | AFRO | WHO Collaborating Centre for Educating Nurses and Midwives in Community Problem-solving | PHIRI Margaret Loma | Active | Details |
| SOA-14 | University of South Africa (UNISA) | Pretoria | SOUTH AFRICA | AFRO | WHO Collaborating Centre for Postgraduate Distance Education and Research in Nursing and Midwifery Development | PHIRI Margaret Loma | Active | Details |
| SOA-17 | South African Medical Research Council | Houghton | SOUTH AFRICA | AFRO | WHO Collaborating Centre for Urban Health | SENKORO Hawa Hamisi | Active | Details |
| SOA-18 | University of Western Cape | Bellville | SOUTH AFRICA | AFRO | WHO Collaborating Centre for Research and Training in Human Resource for Health Development | NYONI Jennifer | Active | Details |
| SOA-19 | University of Cape Town | Cape Town | SOUTH AFRICA | AFRO | WHO Collaborating Centre for Occupational Health | BAGAYOKO Magaran Monzon | Active | Details |
| SOA-23 | University of Fort Hare | East London | SOUTH AFRICA | AFRO | WHO Collaborating Centre for Research Synthesis on Reproductive Health | KHANNA Jitendra | Active | Details |
| SOA-24 | ITOCA-Information Training and Outreach Centre for Africa | Centurion | SOUTH AFRICA | AFRO | WHO Collaborating Centre for training in access and use of electronic Scientific Technological and Medical information | MOUHOUELO Pascal | Active | Details |