Undernutrition continues to contribute substantially to childhood morbidity and mortality in Ethiopia, as elsewhere. In Ethiopia, most studies unraveling the correlates of risk are based on school-based anthropometric surveys of wasting and stunting. Therefore, this study aimed to determine prevalence of undernutrition and detail associated factors among children aged 5–14 years from a population-representative sample of households in the Haramaya District Demographic and Health Surveillance site, Eastern Ethiopia. Data were collected June 30th to July 15th, 2020. A detailed community-based cross sectional survey was conducted among 822 randomly selected children aged 5–14 years, including interviews with mothers/guardians and measurements of children. Wasting and stunting status of children was assessed via anthropometric measurements and WHO Anthro Survey Analyzer was used to analyze Z-score. Multivariable binary logistic regression model was fitted including an array of contextual variables, including highly local considerations such as khat (chat) use. Variables with a p-value<0.05 were declared significant factors associated under-nutrition. The prevalence of stunting and thinness was found to be 22.4% [(95% CI: 19.7, 25.5] and 11.9% [(95% CI: 9.8, 14.3], respectively. Parents Kchat chewing is associated with acute malnutrition (wasting) (AOR (1.43(1.19, 2.97). but not chronic malnutrition (stunting). Children being from poor households [AOR = 1.60, 95% CI: 1.05, 2.42], family size greater than three [AOR = 1.71, 95% CI: 1.13, 2.60], and dietary diversity score three or less food groups [AOR = 1.5, 95% CI: 1.07, 2.13] were significantly associated with stunting. While being in age range of 13–14 [AOR = 2.25, 95% CI: 1.13, 4.47], family size of 4 and above [AOR = 2.60, 95% CI: 1.34, 5.03] and dietary diversity score three or less food groups [AOR = 1.89, 95% CI: 1.17, 3.04] were significantly associated with thinness. The finding of this study showed that there was high prevalence of stunting and thinness among children aged from 5 to 14 years old in Haramaya district. Therefore, all stakeholders should need to strengthen nutritional counseling of family and sensitization of family planning program. • Parents Kchat chewing is associated with acute malnutrition (wasting) but not chronic malnutrition (stunting). • The finding of this study showed that there was high prevalence of stunting and thinness. • Increase family size and poor dietary diversity is related with both thinness and stunting.