The identification of the earliest diagnostic markers for infections in newborns remains one of the priorities in neonatology. In our study, we aimed to assess the diagnostic value of presepsin (P-SEP) as a marker for congenital infections in newborn children. The study was prospective in design and took place from January 2020 to February 2021. We enrolled a total of 64 children with a gestational age of 24 to 40 weeks. The study was approved by the Biomedical Research Ethics Committee (Minutes No.12 of 17 November 2016) and the Scientific Council (Minutes No.19 of 29 November 2016) of the V.I. Kulakov NMRC OGP of Ministry of Healthcare of the Russian Federation. Written voluntary consent to the patients’ participation in the study was obtained from their legal representatives. The patients were divided into 2 groups: a group of interest consisting of newborn children with congenital infections (n = 30), and a control group comprising newborns without signs of infection (n = 34). The group of interest included children with congenital pneumonia (n = 25), urinary tract infections (n = 3), and infections specific to the perinatal period, without a focus of infection (n = 2). Gestational age and birth weight were comparable between the groups. No statistically significant differences in CRP levels, neutrophil counts, immature-to-total neutrophil ratios and lactate concentrations on days 1 and 3 of life were found between the two groups. In the group of interest, P-SEP on day 1 of life was significantly higher than in the control group (р = 0.015). Our findings suggested that P-SEP levels ≥ 481 pg/mL could predict a high risk of congenital infections in newborns. The sensitivity and specificity were 91.0% and 60.0% respectively. P-SEP levels determined in capillary blood were similar to those obtained from venous blood samples suggesting that either can be used for P-SEP measurement with equal success. P-SEP levels were shown to decrease by day 3 of life in the children with congenital infections who had been treated with antibiotics.