Abstract Indirect effects of conflict on mortality of vulnerable groups are as important, or more important, than the direct effects. However, data limitations and methodological challenges hinder the estimation of excess deaths produced by conflict, and few studies explore the mechanisms by which conflict harms civilian populations. We estimate the impact of the Malian conflict on child mortality over the period 2012–2018 using Demographic Health Survey data. We use birth histories to build time series of child mortality, and we employ novel synthetic control methods to show that the Malian conflict significantly increased child mortality in northern Mali. We conduct a difference‐in‐difference analysis of the impact of conflict on key determinants of maternal and child health and conclude that a reduction in access to safe sanitation and to child vaccinations in conflict areas was among the most likely causes of the increase in mortality. Northern Mali is today one of the poorest and most neglected areas of the world where humanitarian assistance is urgently needed.