Background: Thrombocytopenia is one of the most frequent hematologic disorders encountered in the sick neonate. This is evidenced by a fairly high prevalence among neonates admitted to the neonatal intensive care unit 22%-35%, especially in very-low-birth-weight and preterm neonates its prevalence is up to 70%-80%. In Africa, the prevalence of neonatal thrombocytopenia in Nigeria is 53%, 12.4% in Tunisia, and 16.2% in Libya. However, in Ethiopia, there is limited study assessed both its prevalence and associated factors. Objective: to assess the prevalence of thrombocytopenia and its associated factors among neonates admitted to neonatal intensive care unit at public hospitals in Addis Ababa in 2020/21.Method: Institution based cross sectional study was conducted at NICU of selected Addis Ababa public hospitals from February 15thto March 15th, 2021. Single population proportion formula was used to determine sample size. The final sample size was 423. The collected data entered using Epi data and exported to SPSS version 25 for analysis. Variables that have P-value<0.05in bivariable entered in to multivariable logistic regression model to control for confounder. Statistical significance declared at p-value <0.05.Results: The prevalence of neonatal thrombocytopenia in the study area is 66%.In this study variables such as eclampsia(AOR=4.8, 95%CI: 2.66-13.94), Prolonged rupture of membrane(AOR=0.26, 95%CI:0.101-0.669), Intra uterine growth retardation(AOR=0.26, 95%CI: 0.1-0.68), neonatal sepsis (AOR=11.98, 95%CI: 4.023-25.7), Perinatal asphyxia(AOR=6.68, 95%CI: 2.616-17.6), Necrotizing enterocolitis (AOR=14.6, 95%CI: 2.84-35.61) and prolonged nothing per mouth(AOR=0.243,95%CI: 0.084-0.705) were factors associated with neonatal thrombocytopenia.Conclusion and recommendation: Prevalence of neonatal thrombocytopenia in Addis Ababa public hospitals neonatal intensive care unit is high. Therefore, identifying factors associated with it used as an input in reducing the problem.