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Background: Congenital anomalies represent a significant contributor to infant mortality, morbidity, and enduring disability. With this in mind, the present investigation endeavour to ascertain the pooled prevalence of congenital anomalies and associated determinants among neonates in Ethiopia. Method: PubMed, Google Scholar, CINAHAL, Hinari, and Global Health databases were systematically searched. Joanna Briggs Institute (JBI) assessment checklist was used to assess quality of included studies. Data were extracted from database and exported to stataMP-17 for analysis. Pooled prevalence was determined using DerSimonian-Laird random effects model. The degree of heterogeneity and Publication bias were assessed using I2 statistics and Eggers test, respectively. Study protocol was registered under PROSPERO ID CRD42021229140. Result: A total of 18 studies with 519,327 participants were included in the study. Pooled prevalence of congenital anomalies in Ethiopia was 2% (95% CI: 0.02, 0.03%). Among affected newborns neural tube defect (48%) was the most common congenital anomaly in Ethiopia, followed by orofacial cleft (19%). Risk factors such as alcohol consumption (pooled OR: 2.28, 95% CI: 1.54, 3.38), lack of folic acid supplement (pooled OR: 2.83, 95% CI: 1.09–7.36), medication during pregnancy (pooled OR: 2.58, 95% CI: 1.03–6.47), khat (Catha edulis) chewing (pooled OR: 2.44, 95% CI: 1.61–3.71), exposure to pesticides (pooled OR: 4.45, 95% CI: 2.44–8.09) and maternal illness (pooled OR:1.79, 95% CI: 1.03, 3.10) had statistically significant association with congenital anomalies in Ethiopia. Conclusion: In this review, prevalence of congenital anomalies in Ethiopia was high with considerable regional variation. The most common type of congenital anomaly in Ethiopia was neural tube defects, followed by oro-facial cleft. Alcohol consumption, inadequate intake of folic acid, khat chewing, maternal diseases, exposure to pesticides, and use of medication during pregnancy were identified as potential contributors to congenital abnormalities in Ethiopia. [ABSTRACT FROM AUTHOR]