Africa is set to drive future global urbanization, yet the evolution of its urban systems remains underexplored. Here we show this evolution during 1950–2020 using three urban system rules based on a unified urban definition across the African continent. Zipf’s law quantified increasing population concentration in large cities, leading to a shift from dispersed to centralized city-size distributions. As Gibrat’s law predicted, urban population growth was independent of its initial size since the 1990s. Relative growth among different-sized cities changed urban hierarchy, thus the integration of Zipf’s and Gibrat’s laws uncovered imbalances in urban system structures. The third rule we focus on is the scaling law, where unexpected super-linear scaling relationships between built-up areas and population size indicated lower land-use efficiency in large cities, particularly in Eastern and Western Africa. However, the overall decline in built-up scaling exponents over time suggested improving economies of scale as urban systems matured. This study evidenced simple rules behind complex urban systems that help us understand broader urban complexities and urbanization dynamics..