Leishmaniasis is a group of vector-borne, parasitic diseases caused by over 20 species of the protozoan, Leishmania spp. The three major disease classifications, cutaneous, visceral, and mucocutaneous, have a range of clinical manifestations, ranging from self-healing skin lesions to hepatosplenomegaly and mucosal membrane damage to fatality. As a Category I Neglected Tropical Disease, leishmaniasis represents a major international health challenge with over 1 billion people living in disease-endemic areas. As of 2018, cutaneous leishmaniasis is endemic in 92 countries and territories while visceral leishmaniasis is endemic in 83 countries and territories. The first line chemotherapeutics used to treat leishmaniasis are intravenous pentavalent antimonials; however, these drugs have harsh side effects and prolonged, high-cost treatment regimens. Other chemotherapeutics like amphotericin B and miltefosine are being more widely used, but still face many of the same limitations as pentavalent antimonials as well as the emergence of drug resistance. There is an important need for identifying and developing novel chemotherapeutics. We developed a novel, target-free fluorometric high-throughput screen to identify small molecules with anti-leishmanial activity. Of the 10,000 compounds initially screened, 109 molecular scaffolds were represented within the hit compounds; three of these scaffolds warranted further study: 2,4-diaminoquinazoline (2,4-DAQ), 1,4-diaryl-pyrazolo-pyridinone (1,4-DAPP), and pyrazolo[5,1-c][1,2,4]triazine (PTZ). Utilizing mCherry fluorescent Leishmania donovani and Leishmania major in in vitro and in vivo efficacy studies allowed for easy, automated quantification of parasite survival as well as real-time infection monitoring. The 1,4-DAPP and PTZ scaffolds have not been previously identified as anti-leishmanials; even more promising is that only 5 of the 55 analogs we synthesized exhibited any cytotoxic effects. In addition, we optimized both murine ear and footpad infection models of cutaneous leishmaniasis; using fluorescence allowed us to monitor an infection of a single mouse over time. We were able to identify two potent 1,4-DAPP analogs that routinely exhibited efficacy in our in vitro and in vivo models.