Background:The number of children who are left orphaned in the world due to loss of parents has increased in recent years. Ethiopia contains and struggles to care for millions of orphaned children. Orphanages may lack adequate resources to provide adequate necessities including food and healthcare services.Children living in orphanages are more vulnerable to under nutrition as various factors which are linked to child nutritional well–being are more likely to be inadequate. The main objective of this study therefore was to assess the magnitude of under nutrition and associated factors among school-age orphans residing in selected orphanages in Addis Ababa. Methods: A cross sectional, descriptive study design was used and the study was conducted from December 2018 to January 2019. Total of 246 school-age orphans were the study population selected using simple random sampling technique from selected orphanages in Addis Ababa, Ethiopia. The data was collected using pretested and structured institution-based questionnaire. Quantitative data was analyzed using SPSS version 20.0. For qualitative data, an in-depth interview and key informant interview was conducted with care givers and orphanage administrators using semi-structured topic guide, and thematic analysis was applied. Result:The prevalence of underweight, stunting and low BMI for age among the orphans were 10.7%, 19.7 % and 11.5% respectively. Underweight was associated with presence of illness. The odds of underweight in those orphans who were sick in the last two weeks was 3.3 times more likely than those who were not sick (AOR=3.32; 95% CI;(1.31-8.79)). Care givers in the orphanages had good personal and environmental hygienic practice. Conclusion and recommendation:the magnitude of under nutrition among the school- age orphans residing in the five orphanages who were sick in the last two weeks was higher than those who were not sick. There’s a need for the government to support and enforce the orphanages administration to have a strong follow-up protocol for sick children in the orphanage.