This study quantifies the economic costs of climate change impacts on protected areas in Africa. Downscaled results from four Global Circulation Models (GCMs) are used to classify different ecosystems in accordance with the Holdridge Life Zone (HLZ) system. A benefits transfer approach is then used to place an economic value on the predicted ecosystem shifts resulting from climate change in protected areas. The results provide approximations for the impacts on biodiversity in Africa under the “business-as-usual” scenario established by the Intergovernmental Panel on Climate Change (IPCC) for the middle and end of the 21st century. The geographical analysis shows that there are twenty HLZs in Africa and all of them are represented in the protected area network. Three of these HLZs do not change in extent as a result of climate change. Assuming initially that the willingness to pay (WTP) values and the preferences for different ecosystem services remain constant, three of the GCM models show an (undiscounted) negative economic impact of climate change for protected areas in Africa for the year 2100. The worst-case damage scenario totals USD 74.5 million by 2100. However, the model for the year 2065 shows a higher undiscounted value than the present. The finding of positive net impacts from warming is consistent with the predictions of other macro models that show potential gains from warming scenarios.