The emergence of drug-resistant Leishmania is the major challenge to management of visceral leishmaniasis (VL) in areas in which this parasite is endemic. Miltefosine has been widely used against VL, but the emergence of resistant strains could impose a significant threat in the near future. The present study used high-throughput proteomics to determine whether proteins are differentially expressed in miltefosine-resistant (BHU875) and -sensitive (DD8) Leishmania donovani strains. Comparative proteomic analysis revealed up-regulation of iron superoxide dismutase (FeSODA) in the resistant BHU875 strain compared to the drug-sensitive DD8 strain. In accordance with the proteomic data, BHU875 showed higher FeSODA enzymatic activity relative to the sensitive strain. Molecular characterization of BHU875 parasites in which the gene encoding FeSODA was silenced demonstrated that drug sensitivity was restored and the intracellular survival of the parasite was lowered. This suggests that FeSODA activity plays a part in miltefosine resistance. Our study provides a drug target that could be used to overcome miltefosine resistance or help in rational redesigning of miltefosine-based therapy to combat Leishmania infection.