Baccharis mattogrosensis is a species from Asteraceae which has been used in Brazilian folk medicine to treatment of several illnesses, including those caused by parasites. In the present work, the MeOH extract of aerial parts of B. mattogrosensis was subjected to chromatographic fractionation to afford three flavonoids: apigenin (1), quercetin (2), and kaempferol (3) as well as a mixture three chlorogenic acids: 3,4‐O‐dicaffeoylquinic (4), 3,5‐O‐dicaffeoylquinic (5), and 4,5‐O‐dicaffeoylquinic (6) acids. When tested in vitro, kaempferol (3) exhibited activity against Schistosoma mansoni with EC50 = 81.86 μM, whereas compounds 1, 2, 4 – 6 showed to be inactives. Considering this result, the effects of kaempferol (3) against S. mansoni infection using in vivo assay was tested at first time. Using a single oral dose (400 mg/kg) of kaempferol (3) to S. mansoni‐infected mice reduced the worm burden by 25.5%. Similarly, the number of eggs, which are responsible for a variety of pathologies and transmission of schistosomiasis, was decreased by 28.8% in treated mice. Collectively, although kaempferol (3) is partially active when administered orally in a mouse model of schistosomiasis, our results suggest that this compound could be, in future studies, administered in different forms, such as nanoformulation.