Africa, the second largest continent in the world, has achieved remarkable economic and political results through exploration and positive development. Ecological security comprehensively reflects the heath and integrity of an ecosystem, and it is broadly defined as the security state of a complex artificial ecosystem composed of natural, economic and social factors. Ecological security determines the potential for sustainable development in Africa, especially with its rapidly developing economies. However, there is a lack of information on the ecological security state of the continent as a whole. In this study, we constructed an evaluation system based on a pressure-state-response model and evaluated the ecological security state of all 54 African countries. The results showed that, at the national level, the ecological security state of the countries in Africa differed, as did their spatial and temporal variations from 1995 to 2016. In general, African countries showed relatively good ecological security. The years 2007 and 2001 were the worst and best years, respectively, in terms of ecological security during the study period. At the regional level, North Africa and West Africa had the best and worst ecological security, respectively.