Objective: This study aimed to identify the impact of malnutrition on the academic performance of children in Ethiopia. Method: The protocol of this study is registered in PROSPERO with a registration number CRD42021242269. A comprehensive search of studies from HINARY, MEDLINE (via PubMed), EMBASE, Cochrane Library, SCOPUS, Google Scholar, and Google was conducted. All published and unpublished studies conducted about the effect of any forms of malnutrition on academic performance of elementary school children in Ethiopia using the English language were included. Quality of the articles was assessed using the Joanna Briggs Institute critical appraisal tool. The pooled log odds ratio with 95% confidence interval was determined to identify the effect of malnutrition on academic performance. I-square statistics was applied to check the degree of heterogeneity between studies. The presence of publication or small study bias had been assessed by Funnel plots, Egger’s weighted regression test, and Begg’s rank correlation test. Result: A total of 10 studies were included in this study. The pooled prevalence of good academic performance among elementary school students in Ethiopia was 58% (95% confidence interval: 48%, 69%). Stunting (odds ratio = 0.48; 95% confidence interval: 0.30, 0.79), underweight (odds ratio = 0.38; 95% confidence interval: 0.27, 0.53), and iodine deficiency (odds ratio = 0.49; 95% confidence interval: 0.31, 0.78) had a significant association with the academic performance. Rural residence (odds ratio = 0.61; 95% confidence interval: 0.44, 0.83), being female (odds ratio = 0.53; 95% confidence interval: 0.37, 0.77), and uneducated parent (odds ratio = 0.51; 95% confidence interval: 0.44, 0.58) were also factors associated with good academic performance of primary school children in Ethiopia. Conclusion: This study concluded that malnutrition in the form of stunting, underweight, and iodine deficiency affected the academic performance of elementary school children in Ethiopia. So, the Ministry of Health worked better to strengthen the nutrition intervention at the critical periods of brain development.