Background: Neonatal sepsis is one of the most leading causes of inflated death and illness of neonates. Different primary studies in Eastern Africa showed the burden of neonatal sepsis. However, inconsistency among those studies was seen and no review has been conducted to report the amalgamated magnitude and associated factors. Therefore, this review aimed to estimate the national prevalence and associated factors of neonatal sepsis in Eastern Africa. Methods: Using PRISMA guideline, we systematically reviewed and meta-analyzed studies that examined the prevalence and associated factors of neonatal sepsis from PubMed, Cochrane library, and Google Scholar. Heterogeneity across the studies was evaluated using the Q and the I2 test. A weighted inverse variance random-effects model was applied to estimate the national prevalence and the effect size of associated factors. The subgroup analysis was conducted by country, study design, and year of publication. A funnel plot and Egger’s regression test were used to see publication bias. Result: A total of 26 studies with 11239 participants were used for analysis. The pooled prevalence of neonatal sepsis in East Africa was 29.65% (95% CI; 23.36–35.94).Home delivery(AOR =2.67; 95% CI: 1.15-4.00; I2= 0.0%; P=0.996), maternal history of UTI (AOR=2.083; 95% CI :0.24-3.93; I2= 69.1%; P=0.001),gestational age (preterm) (AOR=1.56; 95% CI: 1.04-2.08; I2= 27.8%;P=0.000) ,prolonged labor (AOR=3.23 ;95% CI: -0.04-6.51; I2= 62.7%; P=0.020) and PROM (AOR= 1.95; 95% CI: 0.53-3.37; I2= 43.2%; P=0.062) were identified factors of neonatal sepsis. Conclusions: The prevalence of neonatal sepsis in Eastern Africa remains high. This review may help policy-makers and program officers to design neonatal sepsis preventive interventions. Keywords: Neonatal sepsis, Eastern Africa