We previously reported that the innate sensing of the endosymbiont <i>Leishmania</i> RNA virus 1 (LRV1) within <i>Leishmania (Viannia) guyanensis</i> through Toll-like receptor 3, worsens the pathogenesis of parasite infection in mice. The presence of LRV1 has been associated with the failure of first-line treatment in patients infected with LRV1 containing - <i>L. guyanensis</i> and - <i>L. braziliensis</i> parasites. Here, we established a semi-automated image-based high-throughput drug screening (HTDS) protocol to measure parasiticidal activity of the Prestwick chemical library in primary murine macrophages infected with LRV1-containing <i>L. guyanensis</i> . The two-independent screens generated 14 hit compounds with over sixty-nine percent reduction in parasite growth compared to control, at a single dose in both screens. Our screening strategy offers great potential in the search for new drugs and accelerates the discovery rate in the field of drug repurposing against <i>Leishmania</i> . Moreover, this technique allows the concomitant assessment of the effect of drug toxicity on host cell number.