Toxoplasmosis is a serious zoonotic disease that can lead to abortion and congenital disorders and has a widespread global distribution in humans and animals. The objective of this review was to investigate the incidence of toxoplasmosis in Iranian neonates in order to obtain a comprehensive assessment of the overall situation of the disease for use in developing future interventions. Original studies investigating the incidence of Toxoplasma gondii infections in Iranian neonates were systematically searched in a number of English-language and Persian-language electronic databases. The search process resulted in the inclusion of a total of 11 studies in the systematic review, 10 of which were entered into the meta-analysis. The reviewed articles included 2,230 Iranian neonates investigated through January 1, 2018. Based on the retrieved studies, the overall weighted incidence rates of toxoplasmosis in the Iranian neonatal population and neonates with suspected congenital toxoplasmosis were estimated to be 0.64% (95% confidence interval [CI], 0.31 to 1.09) and 4.10% (95% CI, 2.68 to 5.77), respectively, using a fixed-effects model. The findings of the reviewed studies demonstrate that the incidence of toxoplasmosis is high in Iranian neonates. Accordingly, it can be concluded that toxoplasmosis is a serious public health concern that has been ignored by the Ministry of Health. Therefore, it is essential to perform further studies, in addition to implementing screening and detection programs, using standardized methods to estimate the incidence of toxoplasmosis in Iran and to determine its associated risk factors.