The use of conventional drugs is not a satisfactory treatment for the disease. Therefore, there is a crucial need for alternative therapeutic approaches. This study aimed to investigate the potential anti-leishmanial activity of Gossypium hirsutum niosomes against cutaneous leishmaniasis in a murine model and evaluate their effectiveness by assessing parasite burden, immunomodulatory gene expression, and histopathological profile. We prepared G. hirsutum niosomes and characterized their morphology, size, Fourier transform infrared spectroscopy (FT-IR), and encapsulation efficiency. The in vivo anti-leishmanial activity of the niosomes was evaluated by assessing parasite burden, histopathological profile, and gene expression level. The spleen parasite load in BALB/c mice treated with different groups of G. hirsutum niosomes and G. hirsutum extracts (30%), demonstrated a significant decrease compared to Glucantime®. The least number of leishmanial parasites was observed in H and E-stained histological sections (grade+1), followed by G. hirsutum niosomes or G. hirsutum crude extract (grade+3), Glucantime® (grade+4) and the highest number in the untreated control group (grade+6). There was a substantial difference (P<0.001) among various treatment groups. Moreover, G. hirsutum niosomes up-regulated the levels of the gene (particularly IFN-γ, P < 0.001) compared to the extract form and Glucantime®. In contrast, IL-4, IL-10, and TNF-β were significantly decreased (P < 0.001) in comparison to untreated control. These results suggest that G. hirsutum niosomes have the potential to be considered a promising alternative therapy for leishmaniasis. Further research is warranted to explore their mechanism of action and optimize their formulation for clinical use.