African lion Panthera leo populations have declined as a result of various anthropogenic factors, and most extant populations are small, which further compromises their persistence. Lions in unfenced areas are more exposed to illegal hunting, snaring and poisoning, and populations in fenced reserves are subject to population control by removal of selected individuals from particular age and sex classes. During 2000–2011 19 lions from the mostly unfenced Northern Tuli Game Reserve in Botswana were shot, snared or poisoned. By contrast, only one lioness was shot outside the fenced Venetia Limpopo Nature Reserve 10 km away, in South Africa, where 29 lions were trophy hunted or culled. We found that the mean population size, sex ratio and litter size were the same for both reserves but population density, pride size and cub survival rate were significantly higher in the fenced reserve. The size of the population in Northern Tuli was constrained by a high rate of indiscriminate anthropogenic mortality, with 94.7% of adult mortality occurring outside the reserve. The different forms of anthropogenic suppression in evidence at the two reserves resulted in different population-level responses, which will ultimately affect population viability. As conservation strategies are attempting to remove fences and establish larger conservation areas, this study indicates how fences can influence population dynamics in areas where human presence threatens large carnivores.