Salinomycin (SAL) is a natural polyether ionophore that exhibits a very broad spectrum of biological effects, ranging from anticancer to antiparasitic activities. Our recent studies have shown that the chemical modification of the SAL biomolecule is a fruitful strategy for generating lead compounds for the development of novel antitrypanosomal agents. As a continuation of our program to develop trypanocidal active lead structures, we synthesized a series of 14 novel urea and thiourea analogs of C20-epi-aminosalinomycin (compound 2b). The trypanocidal and cytotoxic activities of the derivatives were assessed with the mammalian life cycle stage of Trypanosoma brucei and human leukemic HL-60 cells, respectively. The most antitrypanosomal compounds were the two thiourea derivatives 4b (C20-n-butylthiourea) and 4d (C20-phenylthiourea) with 50% growth inhibition (GI50) values of 0.18 and 0.22 μM and selectivity indices of 47 and 41, respectively. As potent SAL derivatives have been shown to induce strong cell swelling in bloodstream forms of T. brucei, the effect of compounds 4b and 4d to increase the cell volume of the parasite was also investigated. Interestingly, both derivatives were capable to induce faster cell swelling in bloodstream-form trypanosomes than the reference compound SAL. These findings support the suggestion that C20-epi-aminosalinomycin derivatives are suitable leads in the rational development of new and improved trypanocidal drugs.