Congenital toxoplasmosis (CT) is a rare entity and it may pose a life-threatening risk for the newborns. The aim of the study was to evaluate the incidence and other selected factors of CT in Poland. Our study is a population-based study on CT patients in 2007–2021. The study was based on 1504 hospitalization records of first-time diagnosis of CT in newborns. In the study group, we observed 763 males (50.7%) and 741 females (49.3%). The mean and median age was 31 days and 10 days, respectively. Based on the hospital registry, the mean annual CT incidence was estimated to be 2.6 per 10,000 live births (95% CI 2.0–3.2 per 10,000 live births). The incidence of CT cases fluctuated over the years 2007–2021, with the highest incidence in 2010 and the lowest one in 2014. There were no statistically significant differences between the incidence of CT in relation to sex or place of residence. The periodic fluctuations in the number of cases of congenital toxoplasmosis indicates the need to develop effective prevention programs to effectively counteract the disease and its consequences.