As a part of our project aimed at searching new safe chemotherapeutic agents against parasitic diseases, several compounds structurally related to the antiparasitic agent WC-9 (4-phenoxyphenoxyethyl thiocyanate), which were modified at the terminal phenyl ring, were designed, synthesized and evaluated as growth inhibitors against Trypanosoma cruzi, the etiological agent of Chagas disease and Toxoplasma gondii, the parasite responsible of toxoplasmosis. Most of the synthetic analogues exhibited similar antiparasitic activity being slightly more potent than our lead WC-9. For example, the trifluoromethyl derivatives 15 and 16 exhibited ED50 values of 10.0 μM and 9.2 μM, respectively, against intracellular T. cruzi, whereas they showed potent action against tachyzoites of T. gondii (ED50 values 1.6 μM and 1.9 μM against T. gondii, respectively). In addition, the WC-9 analogues 48 and 61, in which the terminal aryl group was meta with respect to the alkyl chain bearing the thiocyanate group, showed potent inhibitory action against both T. cruzi and T. gondii at the very low micromolar range suggesting that para-phenyl substitution pattern is not necessarily required for biological activity.