The Foundation for Human Rights was established in 1996 through a cooperation agreement between the European Union and the South African Government by signing the European Union Human Rights Programme. The aim of the Foundation is to address the historical legacy of Apartheid, support the transformation of South Africa and to build a human rights culture using the Constitution of South Africa as a tool. It receives funds primarily from the European Union as well as other donors such as DCI, Mott Foundation and Care International. The members of the Supervisory Board of the Foundation are all prominent South Africans, and include representatives of the Department of Justice and Constitutional Development and the European Union.

The first EU-founded programme covered the period between 1996 and 2000 and the second between 2001 and 2007. During the second programme the Foundation has made a few significant changes. The first was a name change from the European Union Foundation for Human Rights to the Foundation for Human Rights- reflecting that Foundation is an indigenous organization. It was also agreed that the Foundation would expand its funding base. The second major change was the recognition that the organization should be lead by a South African - Yasmin Sooka.