BACKGROUND: Armed conflict severely impacts children's health, leading to malnutrition and increased child mortality. The republic of South Sudan gained independence from Sudan in 2011 and suffered from seven-years civil war between December 2013-2021. The war led to mass population displacement both internally and externally and worsened the health status of the population, especially the children. AIM: To investigate the effect of conflict intensity on global acute malnutrition and under-five crude mortality rate in South Sudan during the civil war between 2014-2021. METHODS: The study used an ecological panel data analysis of armed conflict data from Uppsala Conflict Data Program (UCDP) and child health data from Standardized Monitoring and Assessment of Relief and Transitions surveys conducted in 2014-2021. Child health is evaluated as global acute malnutrition (GAM) and under-five crude mortality rate (U5CMR). The study analyzed the correlation between the intensity of conflict and the prevalence of malnutrition and under-five crude mortality on a state level. Internal displacement and food prices were used as indirect effects of conflict. One year lag effect regressions were used to estimate potential correlation between child health and armed conflict. RESULTS: Total number of conflict related deaths between 2014-2021 was on best estimate (9,577), and on high estimate (13,178). The average GAM rate for the same period was (15.29%), and U5CMR was (0.77). Data analysis showed a significant correlation between the high estimate of conflict intensity with GAM (.047), and with U5CMR (.043). Internal displacement and food prices had a significant correlation with GAM (P = .048, P = .016), but no significant correlation was noticed with U5CMR. Best estimate of conflict intensity did not show a significant effect on children health variables. CONCLUSION: The effect of conflict on children's health outcome is complex and multifactorial. The high estimate of conflict intensity from UCDP showed significant correlation with the health outcome, while best estimate did not have significant correlation, this could be due to limited child health data, underreporting of conflict-related deaths, and a small sample size. The study suggests that other factors such as food prices and displacement might play an additional factor that increases the effect of conflict intensity on child health outcomes. The study underscores the challenge of data scarcity in researching health determinants in South Sudan.