Clinical cases of metronidazole resistant Trichomonas vaginalis infections have spurred interest in drug discovery against this protozoal parasite. We have carried out structure-activity studies using mononuclear palladium(II) complexes containing salicylaldiminato thiosemicarbazones on a patient isolate of Trichomonas vaginalis highly resistant to the FDA-approved drug metronidazole. A small library of sixteen compounds were analysed on this resistant isolate. Interestingly, compared with our previous analysis of a metronidazole sensitive strain, susceptibility of this resistant isolate to four of the six most potent compounds was observed. Two compounds had similar IC50 values between the resistant strain and a previously analysed sensitive line. Palladium(II) salicylaldiminato thiosemicarbazone complexes may represent, with further development, a new drug discovery direction for treating clinical cases of metronidazole-resistant T. vaginalis. The most potent compound had an IC50 value of 15 μM on parasite growth and showed no effects on common normal flora bacteria and no morphological effects when tested on cultured mammalian cells.