Background This research examines the relationship between violent conflict and childhood wasting in Northeast Nigeria, where residents have been subjected to fighting between the Nigerian government and Boko Haram - an extremist Islamist movement - since 2009. Methods Using two Demographic and Health Surveys from before and after the Boko Haram insurgency started, a double-difference (difference-in-difference) approach is used to assess the impact of the conflict on mean weight-for-height z-scores and the likelihood of wasting. Results Results suggest that if children exposed to the conflict had not been exposed, their mean weight-for-height z-score would be 0.49 standard deviations higher (p < 0.001) than it is, increasing from − 0.74 to − 0.25. Additionally, the likelihood of wasting would be 13 percentage points lower (mean z-statistic − 4.2), bringing the proportion down from 23% to 10%. Conclusion Descriptive evidence suggests that poor child health outcomes in the conflict areas of Northeast Nigeria may be due to disruptions to social services and increased food insecurity in an already resource poor area. Although other unidentified factors may contribute to both conflict and wasting, the findings underscore the importance of appropriate programs and policies to support children in conflict zones. Electronic supplementary material The online version of this article (10.1186/s13031-018-0136-2) contains supplementary material, which is available to authorized users.