BACKGROUND: In Ethiopia it is documented that 16% of all grade repetitions in primary school and 33.9% childhood deaths are associated with undernutrition. School aged children are often omitted from public health research. Thus, the present study was carried out to find out the prevalence and determinants of pre-adolescent (5-14 years) acute and chronic undernutrition in Lay Armachiho District. METHODS: In this community based cross-sectional study, anthropometrics, individual and household characteristics data were collected from December, 2016 to January, 2017. A total of 848 school aged children (5-14 years) were included in the study. Z-scores for height-for-age (HAZ) and body-mass-index-for-age (BAZ) were calculated to illustrate stunting (chronic undernutrition) and thinness (acute undernutrition), respectively with Anthro Plus software version 1.0.4 using the WHO 2007 growth reference standard. Finally, backward stepwise multivariable logistic regression analysis was carried out to identify factors associated with stunting and thinness, individually. RESULTS: The overall prevalence of stunting and thinness was 35.5 and 9.9%, respectively. The multivariable analysis showed that child age 10-14 years [AOR = 1.58, 95% CI: 1.17, 2.12] and lack of availability of a latrine at home [AOR = 1.60; 95% CI: 1.17, 2.20)] were associated with increased likelihood of stunting. Nevertheless, child's hand washing practice before eating [AOR = 0.67; 95% CI: 0.49, 0.91] was protective against stunting. Children who consumed diversified foods [AOR = 0.64; 95% CI 0.39, 0.97] were protected from thinness. CONCLUSION: In Lay Armachiho district, one-third and one in every ten of school aged children were stunted and thin, respectively. Children age 10-14 years, lack of availability of a latrine at home and hand washing practices before eating were associated with stunting, while only dietary diversity was associated with thinness. Ensuring consistent hand washing practices before eating and ensuring availability of latrine should be improved in the region, which can assist in effectively tackling undernutrition. Finally, dietary diversification should be enhanced to rectify burden of acute undernutrition.