JRS Southern Africa is currently present in Malawi, South Africa, Angola, and Zimbabwe. The regional office is located in Johannesburg, South Africa.

Southern Africa faced a number of conflicts in former Rhodesia and Namibia during the Apartheid era. Angola and Mozambique suffered civil wars and bitter power struggles following their sudden independence from Portugal in 1975. Decades of conflict, exacerbated by the influence of the Apartheid in nearby South Africa, destroyed both countries. Over time, tensions in the region were eased and stability gradually attained. As a result of several peace negotiations and the end of the Apartheid era, democratic elections were held in Angola and Mozambique in 1992, followed by South Africa in 1994.

In the midst of this context, JRS Southern Africa was established to respond to the needs of hundreds of thousands of Mozambicans fleeing into Zimbabwe and Malawi. At the same time, tens of thousands of refugees were fleeing from unrest, chiefly in areas such as Eastern Africa and the neighbouring Great Lakes Region, to South Africa. To this day, efforts in this region continue to focus on emergency assistance, education, livelihoods, and legal support.