BackgroundMother-To-Child-Transmission (MTCT) of Human Immunodeficiency Virus (HIV) occurs during pregnancy, delivery and breastfeeding, and cause infection among several new-borns. However, there is limited recent evidence on the burden of MTCT of HIV in Ethiopia from a large-scale data. Thus, this study aimed to determine the positivity rate, trend and associated risk factors of MTCT among HIV-exposed infants.MethodologyA cross-sectional study was conducted among 5,679 infants whose specimen referred to Ethiopian Public Health Institute HIV referral laboratory for Early Infant Diagnosis (EID) from January 01, 2016, to December 31, 2020. Data were extracted from the national EID database. Frequencies and percentages were used to summarize the data on characteristics of infants. Logistic regression analysis was employed to identify factors associated with positivity rate of MTCT of HIV. Level of significance was set at 5%.ResultsThe mean age of the infants was 12.6 (± 14.6) weeks with an age range of 4 to 72 weeks. Half of the infants (51.4%) were female. The positivity rate of MTCT decreased from 2.9% in 2016 to 0.9% in 2020 with five-year average positivity rate of 2.6%. HIV test after six weeks (Adjusted odds ratio (AOR) = 2.7; 95% confidence interval (CI): (1.8–4.0,));p<0.001), absence of prevention of mother-to-child-transmission (PMTCT) service (AOR = 4.6; 95% CI: (2.9–7.4));p=0.001), nevirapine prophylaxis not received (AOR = 2.0; 95% CI: (1.3–3.2));p<0.001), and unknown ART status of the mother at delivery (AOR = 11; 95% CI: (5.5–22.1));p<0.001)were significantly associated with MTCT of HIV.ConclusionThe positivity rate of MTCT of HIV was showing declining tendency gradually in the study period. Strengthening PMTCT service, early HIV screening and starting ART for pregnant women, and early infant diagnosis are required to reduce the burden of HIV infection among infants exposed to HIV.