This study aimed to evaluate the leishmanicidal activity of ethanol extract, fractions, and isolated substance from Handroanthus serratifolius against Leishmania amazonensis. Furthermore, this activity was related to cytotoxicity, and the selectivity index was determined. The ethanol extract was obtained by maceration of the stem powder, and the extract was subjected to fractionation on chromatographic column. The lapachol was obtained by acid base extraction followed by purification in chromatographic column. The antipromastigote activity and cytotoxicity tests were carried out by the cell viability method (MTT). Modified THP-1 cells were infected with L. amazonensis promastigotes and treated for 24 h with different concentrations of the extract, fractions, and lapachol. The ethanol extract, dichloromethane, and ethyl acetate fractions were not active against promastigotes (IC50 > 200 μg/mL) or cytotoxic (CC50 > 500 μg/mL), and the selectivity index (SI) was greater than 2.5. The ethyl acetate fraction was active only in promastigotes; it is not cytotoxic (CC50 > 500 μg/mL, SI > 5). The lapachol was selectively active only against amastigote (IS > 2.5, CC50 > 500 μg/mL). In summary, lapachol and ethyl acetate fraction are promising against amastigote and promastigote forms, respectively.