Neglected tropical diseases (NTDs) affect more than a billion people worldwide, mainly populations living in poverty conditions. More than 56% of annual NTD deaths are caused by Leishmaniasis, Sleeping sickness, and Chagas disease. For these three diseases, many problems have been observed with the chemotherapeutic drugs commonly used, these being mainly resistance, high toxicity, and low efficacy. In the search for alternative treatments, hybridization is an interesting approach, which generates new molecules by merging two pharmacophores and then looking for improvements in biological activity or reduced compound toxicity. Here, we review various studies that present such hybrid molecules with promising in vitro and in vivo activities against Leishmania and Trypanosoma parasites.