There exist some concern regarding the sustainability of the production of R&D output and R&D capacity in South Africa. Recent trends indicated evidence of disinvestments and decay of South Africa’s R&D capacity. Questions arise concerning the detrimental effects these trends could have on South Africa’s ability to generate R&D output. As problems are addressed insufficiently and the system is allowed to decay, the costs of rebuilding the system might increase even further. The main research of objective of this thesis is to develop a computer simulation program of R&D performance and the creation of R&D output in the NSI. This model will in turn produce a tool to be used for policy testing, what-if scenario testing or policy optimisation. The purpose of the model is to simulate R&D output generated in the South African system of innovation and to model and explain the effect the presence/lack of long-term investment in R&D and R&D resources could have on the system’s ability to produce R&D output. In developing this model and by using the corresponding simulation programme, decision-makers in government and industry are provided with a tool to analyse policy alternatives. The model will provide a better understanding of the interrelationships between different elements of the NSI, in particular those interacting as funders and performers of R&D. This model will also aid decision makers in enhancing the efficiency of addressing problem areas within the South African R&D system. The contribution made by this thesis to the body of knowledge is that the development of a system dynamic model will result in the establishment of a dynamic hypothesis of the development of new knowledge through R&D in an R&D performing sector. The dynamic hypothesis will in turn lead to a method for modelling the effect of R&D investment on the development of an R&D capacity, i.e. the system’s ability to absorbed knowledge and produce R&D output. The above is essentially a dynamic description of the process around creating and absorbing knowledge through R&D activities.