Background: Although orphans are at increased risk of undernutrition, studies assessing prevalence of undernutrition are limited to orphans residing with their relatives or on street. This study was conducted to assess magnitude of undernutrition and its associated factors among institutionalized school-age orphans in Harari Regional State, eastern Ethiopia. Methods: An institution based cross-sectional study was conducted among all school-age (6-12 years) orphans living in all orphan centers in Harari Regional State, eastern Ethiopia. Data were collected by using a structured pretested questionnaire supplemented with anthropometric measurements. Data were entered using EpiData 3.1 and analyzed using SPSS 22. Logistic regression models were fitted to identify factors associated with undernutrition. Statistical significance was declared at P-value <.05. Results: A total of 265 orphans residing in all orphan centers in the region were included. The prevalence of stunting, wasting, and underweight were 15.8% (95% CI: 11.9, 20.7), 10.9% (95% CI: 7.7, 15.3), and 8.7% (95% CI: 4.3, 10.5), respectively. Staying in orphan center for 6 to 10 years (AOR = 6.2; 95% CI: 2.6, 15.10), having recent illness (AOR = 3.9; 95% CI: 1.4, 10.4), and being aged 10 to 12 years (AOR = 11.2; 95% CI: 3.5, 35.4) were significantly associated with stunting whereas having recent illness (AOR = 4.3; 95% CI: 1.4, 7.3) and being aged 6 to 7 years (AOR: 10.4; 95% CI: 3.2, 33.6) were significantly associated with wasting. Underweight was more likely (AOR: 8.9; 95% CI: 2.7, 29.5) among children with recent illness. Conclusions: Almost 1 in 6, 1 in 9, and 1 in 11 institutionalized school-age orphans in Harari Regional State were stunted, wasted, and underweight respectively. Younger children and those with recent illness were more likely to be undernourished. Underlying reasons for undernutrition among orphans being cared in orphan centers should be further explored.