Child malnutrition is the leading public health problem in Sub-Saharan Africa, resulting in poor health and economic losses. Ethiopia has one of the highest child undernutrition rates in the world that occurs to multifaceted factors, including food insecurity. Thus, we performed a cross-sectional study to assess the prevalence and risk factors for child undernutrition in largely food insecure areas of Ethiopia. Data were collected from 354 mother–child pairs from the Siraro district. Both bivariate and multivariate logistic regression was used for statistical analysis. Variables with a P-value of <0⋅05 in multivariate analysis were used to detect statistical significance at a 95 % confidence level. About 67 % of households are food insecure. The prevalence of stunting wasting and underweight were 42⋅7, 9⋅9 and 27⋅7 %, respectively. Female gender, higher age of the child (12–23 months v. 6–11 months), living in a household with five or more siblings, not getting therapeutic zinc supplement at least once, inadequate diet diversity, lack of growth monitoring service, and maternal own income increases the likelihood of child undernutrition. It can be concluded that child undernutrition is a severe public health problem in the study area. Improving primary healthcare services related to zinc supplementation, growth monitoring and promotion, and improving infant and child feeding practices can be considered as a strategy to address the problem.