Abstract Background Undernutrition remains a major public health concern affecting both children and adolescents in Ethiopia. However, little attention has been given to the undernutrition of primary school-aged children, with their exclusion within national surveys. Therefore, this systematic review and meta-analysis was conducted to determine pooled estimate and determinant factors of undernutrition among primary school-aged children (6 to 15 years of age) in Ethiopia. Method We systematically retrieved available articles on the prevalence of undernutrition in primary school-aged children in Ethiopia by using a number of computerized databases, including PubMed, Scopus, Cochrane Library, Google Scholar, and Science Direct between September 1 and November 25, 2019. Two authors independently extracted relevant data using a standardized data extraction form. Heterogeneity among included studies was assessed with the Cochrane Q test statistics and Higgins I² tests. The pooled estimates and determinant factors of school-aged undernutrition were assessed with random-effects model using Stata/se Version 14. Result We have retrieved 30 eligible articles with pooled sample size of 16,642 primary school- aged children to determine the prevalence of undernutrition in Ethiopia. Hence, the pooled prevalence of stunting, underweight, and wasting were found to be 21.3% (95% CI: 17.0, 25.5), 18.2% (95% CI: 14.4, 22.0) and 17.7% (95% CI, 13.5, 21.8) respectively. Heterogeneity was assessed by doing subgroup analysis for study province/region. Thus, the highest prevalence of stunting was 27.6% (95% CI, 20.7, 34.5) and underweight 22.7% (95% CI, 19.2, 26.3) in Amhara Region while, in the instance of wasting, it was 19.3%(95% CI: 5.1, 33.4) in Southern Nations, Nationalities and People’s Region. Maternal educational status (OR = 1.91, 95% CI: 1.33, 2.73), age of school-aged child (OR = 0.56, 95% CI: 0.44, 0.72) and sex of school-aged child (OR = 0.73, 95% CI: 0.62, 0.85) were found to be significantly associated with stunting. Maternal educational status (OR = 0.6, 95% CI: 0.36, 0.9) and age of school-aged child (OR = 2.74, 95% CI: 1.81, 4.14) were associated with thinness/wasting. Parasitic infection (OR = 2.02, 95% CI: 1.10, 3.73) were associated with underweight of school age children. Conclusion The prevalence of stunting and underweight among primary school-aged children are moderately high while acute undernutrition (wasting) is more critical than under-five national average as reported in the 2016 Ethiopian Demography and Health Survey. Therefore, this finding warrants the need to design a school-aged children nutrition survey and expand school feeding programs to improve the nutritional status of primary school-aged children in the country. In addition, emphasis should be given to female school-aged children in the early school years, creating awareness for those mothers who lack formal education, and preventing and treating/deworming parasitic infection. Moreover, researchers must conduct research in province/regions which have not yet studied school aged children’s nutritional status to date.