Two obligate intracellular parasites, Trypanosoma cruzi, agent of Chagas disease, and Toxoplasma gondii, agent of toxoplasmosis, upregulate the mevalonate pathway of their host cells upon infection, suggesting that this host pathway could be a potential drug target. In this work we designed, synthesized and evaluated the effect of a number of compounds structurally related to WC-9 (4-phenoxyphenoxyethyl thiocyanate), a known squalene synthase inhibitor, on T. cruzi and T. gondii growth in tissue culture cells. The fluorine-containing derivatives 3-(3-fluorophenoxy) and 3-(4-fluorophenoxy)phenoxyethyl thiocyanates exhibited EC50 values of 1.6 µM and 4.9 µM, respectively, against tachyzoites of T. gondii, while they showed similar potency as WC-9 against intracellular T. cruzi (EC50 values 5.4 µM and 5.7 µM, respectively). In addition, 2-[3-(phenoxy)phenoxyethylthio]ethyl-1,1-bisphosphonate, which is a hybrid inhibitor containing 3-phenoxyphenoxy and bisphosphonate groups, has activity on T. gondii proliferation at sub micromolar levels (EC50 = 0.7 µM), suggesting combined inhibitory effect of the two functional groups.