The quest of South Africa to develop, advance, and preserve Indigenous Knowledge Systems (IKS) is an important and necessary endeavour. In South Africa, protecting and advancing IKS is essential to attaining development, empowerment, and equity. IKS is a strategy that can also be applied to promote human rights, preserve nature, improve health, and lessen poverty. As a result, due to the identification and recognition of the potential of Indigenous Knowledge Systems, governmental frameworks for their protection and development have been formed in South Africa. National Indigenous Knowledge Systems (IKS) Policy of 2004 was enacted by the South African government in 2004 as a means of identifying, promoting, and safeguarding IKS in South Africa. The Department of Science and Technology (DST) now known Department of Science and Innovation (DSI) developed the National Recordal System (NRS) through the National Indigenous Knowledge Systems Policy Framework in order to organize and standardize the collection, preservation and dissemination of science and technology-related data on IKS in South Africa. The DSI passed an additional IKS Bill in 2014, which became an IK Act in 2019, to improve the management of IKS in South Africa even more. Using secondary data sourced from government document and existing scholarly works, this study examines how indigenous knowledge systems are protected in South Africa and whether or not they are in line with the government's established Policy and protocol frameworks. It further examines the challenges and prospects the government has faced in protecting South Africa's indigenous knowledge systems. The study also outlines plans and future objectives for advancing indigenous knowledge development in South Africa.