Low nitrogen (N) fertilization is a dominant cause of malnutrition in Africa, but the spatial and temporal variability of N cycling patterns in Africa remain unclear. This study is the first to perform a detailed analysis of the N cycling patterns of 52 African countries from 1961 to 2016. We calculated the N use efficiency (NUE) in crop production, country-specific N fertilization trends, and the impacts of N fertilization on human protein demand and the environment. Over the past five decades, total N input to African croplands increased from 20 to 35 kg N ha−1 yr−1, while the application of synthetic N fertilizers (SNF) increased from 4.0 to 15 kg N ha−1 yr−1. N contributions from animal manure and biological N fixation remained lower than 10 kg N ha−1 yr−1 and 20 kg N ha−1 yr−1, respectively. The total N crop production increased from 15 to 22 kg N ha−1 yr−1 from 1961 to 2016. Total N surplus in Africa increased from 5 to 13 kg N ha−1 yr−1, while estimated gaseous losses increased from 4.0 to 11 kg N ha−1 yr−1. However, NUE declined from 74% to 63% during the past five decades, and protein consumption increased from 2.99 to 3.78 kg N capita−1 yr−1.