We consider the effects of climate change on seasonally migrant populations that herd livestock—i.e., transhumant pastoralists—in Africa. Traditionally, transhumant pastoralists benefit from a cooperative relationship with sedentary agriculturalists whereby arable land is used for crop farming in the wet season and animal grazing in the dry season. Rainfall scarcity can disrupt this arrangement by inducing pastoral groups to migrate to agricultural lands before the harvest, causing conflict to emerge. We examine this hypothesis by combining ethnographic information on the traditional locations of transhumant pastoralists and sedentary agriculturalists with high-resolution data on the location and timing of rainfall and violent conflict events in Africa from 1989–2018. We find that reduced rainfall in the territory of transhumant pastoralists leads to conflict in neighboring areas. Consistent with the proposed mechanism, the conflicts are concentrated in agricultural areas; they occur during the wet season and not the dry season; and they are due to rainfall’s impact on plant biomass growth. Since pastoralists tend to be Muslim and agriculturalists Christian, this mechanism accounts for a sizable proportion of the rapid rise in religious conflict observed in recent decades. Regarding policy responses, we find that development aid projects tend not to mitigate the effects that we document. By contrast, the effects are reduced when transhumant pastoralists have greater power in national government, suggesting that more equal political representation is conducive to peace.