The current study aimed to evaluate the anti-leishmanial activity of sanguinarine and nano chitosan (CS NPs) on Leishmania major, potentially mediated through gene expression of TNF-α and iNOS. To identify the potential targets for sanguinarine, the energy-minimized structure was docked using AutoDock 4.3 software into the active sites of selected peterdin reductase (PTR1) and arginase (ARG-L), which were modeled using homology modeling programs. The colorimetric MTT assay was used to determine the viability of L. major promastigotes subjected to different concentrations of sanguinarine and CS NPs in a concentration- and time-dependent manner. Reactive oxygen species (ROS) levels were measured in treated promastigotes. TNF-α and iNOS expression was determined in PBMCs infected at 24, 48, and 72 h after treatment with sanguinarine and CS NPs. The sanguinarine - PTR1 and ARG-L interactions and calculated energy of these enzymes indicated an excellent affinity for sanguinarine with both enzymes. The IC50 values of the sanguinarine in combination with 10% CS NPs) were 124.76 and 89.25 μM after 24 and 48 h, respectively. Sanguinarine-CS NPs enhanced the expression of TNF-α and iNOs in L. major-infected PBMCs after 24 h (p < 0.05). Sanguinarine-CS NPs could therefore reflect a promising anti-leishmanial agent. Sanguinarine and CS NPs in combination significantly inhibited the proliferation and viability of L.major promastigotes whilst concurrently regulating the expression of TNF-α and iNOS and increasing ROS levels. To better understand the effect of CS NPs and sanguinarine on leishmaniasis, further studies are required in an experimental murine model.