Chagas disease and Leishmaniasis are among the most important parasitic diseases. They are considered to be within the most relevant group of neglected tropical diseases and have been included as priorities for searching new drugs due to their several treatment limitations. These parasitic diseases caused by flagellated protozoans affect more than 20 million people predominantly in developing countries. In this study, we prepared a series of 2-substituted 1,4-benzenediols by an efficient, green, and lithium salt-free synthesis in water/ethanol as solvent to test their anti-parasitic activity. All 36 phenolic derivatives were evaluated in vitro for their activity against T. cruzi epimastigotes, L. infantum, and L. braziliensis promastigotes, as well as their cytotoxicity on macrophage and fibroblast cell lines. Based on the results obtained, the compounds that presented a methyl, trifluoromethyl or bromo group at the para-position of the second benzene ring were found the most active analogs, with higher selective index values on the three parasites assayed. This evidence suggests that the anti-parasitic activity observed in these analogs is affected by the size of the group at the 4-position of the second ring, but not related with electronic factors.This study identified hit compounds with the potential to target several kinetoplastid parasites.