Abstract Background Due to climate changes, immigration, and globalization, Chagas Disease (CD) also afflicts nations without vector transmission. In Europe, congenital CD (cCD) is a significant public health issue, perpetuating the disease: it is crucial to perform CD screening in pregnant women at risk, as the treatment of infants is effective in eradicating the infection. Only a few European regions have a definite algorithm for diagnosing cCD, but no official guidance has been published at the national or European level. To support policymakers, this study aims to outline a cost-effectiveness analysis of CD screening in non-endemic areas, such as Italy, in pregnant women born or arriving from endemic countries and in their newborns. Methods To measure the economic impact of cCD screening, a decision tree model will be used to compare the test option (screening, diagnosis, treatment, follow-up) with no test option (no screening, progression of disease). Model parameters will be taken from relevant scientific literature. The primary outcome will be the Incremental Cost-Effectiveness Ratio (ICER) between the two options. Sensitivity analyses will be conducted to determine how changes in prevalence, transmission rate, screening adherence, and treatment adherence may affect the ICER. Results We expect the ‘test’ option to be cost-effective even with significant reductions in prevalence, transmission rate, adherence to screening or treatment. Threshold levels of these variables will allow to critically extend the results to areas with reduced immigration, patchy distribution of migrants at risk, health logistical limitations, and limited access to care for immigrants. Conclusions Our findings can help policymakers implement official screening programs and diagnostic algorithms for cCD in Italy and other non-endemic countries. This contributes to SDG 3 by combating the spread and burden of neglected tropical diseases and contributing to maternal, child, and migrant health. Key messages • Screening for congenital Chagas Disease in a non-endemic area may be cost-effective and cost-saving. • Study findings could provide useful information for health policymakers to combat Chagas Disease in Europe.