This article analyzes in-depth the development trajectory of the innovation systems (IS) in the case of Namibia. The research data consists of documents, interviews and studies related to IS development in Namibia from the 1990s until early 2016. The case study highlights the spatiotemporal challenges of creating an IS in a developing country with limited STI resources and the potential mismatch between related strategies and practices. IS is a broad framework that identifies and maps potential relevant actors for innovation development but it does not necessary enhance interactions between the actors of IS. For developing countries, the doing-using-interacting mode of innovation fits better when the aim is to integrate indigenous knowledge (IK) into an IS. An IK-included IS can facilitate participatory development processes, foster socioeconomic resilience of local communities and enhance the comparative advantage of a developing country.