Chagas disease is one of the major health problems in Central and South America, which is caused by the parasitic protozoa, Trypanosoma cruzi. It is commonly transmitted by members of blood-sucking subfamily Triatominae. Chagas disease is associated with cardiac and gastrointestinal manifestations. Up to now, there are no effective vaccines for treatment of Chagas disease and benznidazole and nifurtimox are the only effective anti-Chagas drugs that cause different adverse and side effects. Therefore, much attention has been paid to natural products as novel therapeutic strategies for Chagas disease and its manifestations. Nowadays, some flavonoids could be considered as effective and safe bioactive natural products with potential anti-Chagas activity. Despite the increasing evidence, there is lack of review papers regarding the beneficial effects of flavonoids against Chagas disease and its manifestations. The aim of this paper is to review the available scientific data on the beneficial effects of flavonoids on Chagas disease and its manifestations published over the past two decades. Moreover, we provide an overview on etiology, transmission, epidemiology, clinical manifestations, and current treatment protocols of Chagas disease.