In pursuit of potential agents to treat Chagas disease and leishmaniasis, we report the design, synthesis, and identification novel naphthoquinone hydrazidebased molecular hybrids. The compounds were subjected to in vitro trypanocide and leishmanicidal activities. N'-(1,4-Dioxo-1,4-dihydronaphthalen-2-yl)-3,5dimethoxybenzohydrazide (13) showed the best performance against Trypanosoma cruzi (IC 50 1.83 µM) and Leishmania amazonensis (IC 50 9.65 µM). 4-Bromo-N'-(1,4-dioxo-1,4dihydronaphthalen-2-yl)benzohydrazide ( 16) exhibited leishmanicidal activity (IC 50 12.16 µM). Regarding trypanocide activity, compound 13 was low cytotoxic to LLC-MK2 cells (SI = 95.28). Furthermore, through molecular modeling studies, the cysteine proteases cruzain, rhodesain and CPB2.8 were identified as the potential biological targets.