The W-Arly-Pendjari (WAP) ecosystem, shared among Benin, Burkina Faso and Niger, represents the last lion stronghold of West Africa. To assess the impact of trophy hunting on lion populations in hunting areas of the WAP, we analyzed trends in harvest rates from 1999 to 2014. We also investigated whether the hunting areas with higher initial hunting intensity experienced steeper declines in lion harvest between 1999 and 2014, and whether lion densities in hunting areas were lower than in national parks. Lion harvest rate remained overall constant in the WAP. At initial hunting intensities below 1.5 lions/1000km2, most hunting areas experienced an increase in lion harvest rate, although that increase was of lower magnitude for hunting areas with higher initial hunting intensity. The proportion of hunting areas that experienced a decline in lion harvest rate increased at initial hunting intensities above 1.5 lions/1000km2. In 2014, the lion population of the WAP was estimated with a spoor count at 418 (230–648) adults and sub-adult individuals, comparable to the 311 (123–498) individuals estimated in the previous 2012 spoor survey. We found no significant lion spoor density differences between national parks and hunting areas. Hunting areas with higher mean harvest rates did not have lower lion densities. The ratio of large adult males, females and sub-adults was similar between the national parks and the hunting areas. These results suggested that the lion population was not significantly affected by hunting in the WAP. We concluded that a quota of 1 lion/1000km2 would be sustainable for the WAP. Based on our results, an import embargo on lion trophies from the WAP would not be justified. It could ruin the incentive of local actors to conserve lions in hunting areas, and lead to a drastic reduction of lion range in West Africa.