Following the political changes in the early 1990s, senior physicists in South Africa saw the advantages of collaborating with CERN, particularly for the training of young scientists. In 1992, CERN signed a International Cooperation Agreement (ICA) with the Foundation for Research Development (FRD) concerning the further development of scientific and technical cooperation in the research projects of CERN.

CERN has hosted doctoral students, summer students and high-school teachers from South Africa. Previous participation in fixed-target experiments and ISOLDE has evolved to include membership in ALICE and ATLAS.

The South African ALICE team from the University of Cape Town and iThemba LABS is led by people trained at CERN, contributing successfully to software and simulation work on the ALICE dimuon spectrometer, and is deploying Grid technology in South Africa. A joint team from the Universities of Johannesburg and Witwatersrand joined ATLAS in July 2010. CERN and South Africa also collaborate in theoretical physics and through iThemba LABS also in accelerator technologies.

An event commemorating the tenth anniversary of the official launch of the CERN-South Africa programme took place at iThemba LABS in November 2018, highlighting the important South African involvement in CERN and pointing to opportunities for further enhancement.