Abstract: The association of conflict and child health indicators in Nepal was examined for the period of the Communist Party of Nepal–Maoist (CPN-Maoist) insurgency (1996–2006). National and subregional trends in neonatal protection against tetanus, measles and diphtheria–pertussis–tetanus (DPT) vaccine coverage, infant mortality, under-5 mortality, and proportion of underweight or stunted children were examined. During the period of the insurgency there were overall improvements in vaccination coverage; however, measles vaccine and DPT coverage remained static during several years of conflict. A decline in infant and under-5 mortality rates occurred: however, there were smaller improvements in stunting and underweight children. Improvements in health indicators from the Mid-western Hill subregion of the country, an area that was consistently conflict-affected, were less than those achieved nationally or by the less-affected Eastern Hill subregion. In comparison with Bangladesh and India, improvements in Nepal were the same or better, except for stunting and underweight children. Health interventions that are more easily delivered, such as vaccination, showed improvements, although the changes were less in a region of high conflict. Improvements in child nutrition indicators that necessitate multiple, coordinated interventions and access to at-risk populations over time as well as ongoing food security were not as successful. Continued commitment to development of systems for delivery of child health is important to gain improvements across all childhood health indicators.