Background Human immunodeficiency virus (HIV) is one of the most important global health problems. More than one and half million of children are living with HIV in the world, and majority of them are found in sub-Saharan Africa. There are primary fragmented study findings, and no review was conducted with regard to vertical HIV infection in East Africa. Therefore, this review aimed to assess the prevalence of vertical HIV infection and its risk factors among HIV-exposed infants in East Africa. Main body Eligible studies were retrieved by relevant search terms in CINHAL, Pub-MED, Google Scholar, EMBASE, Web of Science, SCOPUS, Cochrane, African Journals Online databases, and Ethiopian University research repositories. Data were extracted with Microsoft Excel and analyzed with Stata version 11 software. The random effect model was used to estimate the pooled prevalence of vertical HIV infection in East Africa. The variation between studies was quantified with an I2 statistic test. Furthermore, sub-group and meta-regression analyses were done to identify the sources of heterogeneity between the studies. The publication bias was assessed by Egger test. This systematic review and meta-analysis have included a total of 33 research articles. The overall pooled prevalence of vertical HIV infection in East Africa was 7.68% with a 95% confidence interval [CI]: (6.23, 9.12) with a heterogeneity of I2 = 86.8 with a p value < 0.001. In subgroup analysis, the pooled prevalence of vertical HIV infection in cross-sectional studies was 6.58%, while in cohort studies were 9.37%. Mixed feeding, AOR = 6.22 (1.02, 11.41); home delivery, AOR = 2 (1.01, 3); mothers took ART less than 4 weeks, AOR = 1.92 (1.79, 2.06); and infants who have not received ARV prophylaxis, AOR = 2.02 (1.05, 2.98) were the associated factors for vertical HIV infection for exposed infants. Conclusions The pooled prevalence of the mother to child transmission of HIV is way more than the desired target of the World Health Organization, which is less than 5% in breastfeeding populations. Thus, strengthening the prevention of vertical HIV transmission, promotion of exclusive breastfeeding, timely initiation of ART prophylaxis for HIV exposed infants, encouragement of hospital delivery, and the start of ART at the time of diagnosis of every HIV-positive person may all reduce the transmission of vertical HIV infection.