Six extracts from the roots and the aerial parts of Waltheria indica L. (Malvaceae) were screened for their in vitro antitrypanosomal activity towards Trypanosoma brucei brucei STIB 427 strain, T. brucei rhodesiense STIB 900 and Trypanosoma cruzi Tulahuen C4. The dichloromethane extract from the roots showed the highest activity against T. cruzi (IC50=0.74 μg/mL) as well as a good selectivity index (SI value of 35). Based on these results, this extract was fractionated and led to the isolation of three alkaloids (adouetin X (1), waltheriones A (2) and C (3)) and three pentacyclic triterpene derivatives (betulinic acid (4), 3β-acetoxy-27-trans-caffeoyloxyolean-12-en-28-oic acid methyl ester (5) and 3β-acetoxy-27-cis-caffeoyloxyolean-12-en-28-oic acid methyl ester (6)) identified by 1D and 2D NMR, UV, IR and MS analyses. Among these, waltherione C exhibited the highest and selective antitrypanosomal activity towards T. cruzi (IC50=1.93 μM) with low cytotoxicity (IC50=101.23 μM), resulting in a selectivity index value of 52. Waltherione C conforms to hit activity criteria with respect to T. cruzi as required by the WHO/TDR.