Twenty nine original 3-nitroimidazo[1,2-<i>a</i>]pyridine derivatives, bearing a phenylthio (or benzylthio) moiety at position 8 of the scaffold, were synthesized. <i>In vitro</i> evaluation highlighted compound <b>5</b> as an antiparasitic hit molecule displaying low cytotoxicity for the human HepG2 cell line (CC<sub>50</sub> > 100 μM) alongside good antileishmanial activities (IC<sub>50</sub> = 1-2.1 μM) against <i>L. donovani</i>, <i>L. infantum</i>, and <i>L. major</i>; and good antitrypanosomal activities (IC<sub>50</sub> = 1.3-2.2 μM) against <i>T. brucei brucei</i> and <i>T. cruzi</i>, in comparison to several reference drugs such as miltefosine, fexinidazole, eflornithine, and benznidazole (IC<sub>50</sub> = 0.6 to 13.3 μM). Molecule <b>5</b>, presenting a low reduction potential (<i>E</i>° = -0.63 V), was shown to be selectively bioactivated by the <i>L. donovani</i> type 1 nitroreductase (NTR1). Importantly, molecule <b>5</b> was neither mutagenic (negative Ames test), nor genotoxic (negative comet assay), in contrast to many other nitroaromatics. Molecule <b>5</b> showed poor microsomal stability; however, its main metabolite (sulfoxide) remained both active and nonmutagenic, making <b>5</b> a good candidate for further <i>in vivo</i> studies.