Due to the presence of a high concentration of surfactants (e.g., Cremophor EL, Tween 80), paclitaxel (PTX) drug delivery systems administered orally and intravenously demonstrate severe toxicity. In the current research work, a unique self-nanoemulsifying drug delivery system (SNEDDS) comprising surfactin, a microbial biosurfactant was used for reducing the formulation toxicity and improving the biopharmaceutical performance. The preformulation study including solubility analysis indicated suitability of corn oil as the natural lipophile. Nanoemulsion boundaries were delineated by aqueous titration of the lipid phase (ethyl oleate: plurol oleique), surfactants (Tween 80 and Surfactin) and cosolvent (Transcutol HP) to identify the optimum compositions on the basis of formulation quality attributes with globule size <250 nm, emulsification time <3 min and in vitro drug release >85% in 60 min. Biocompatibility evaluation of PTX-Surfactin SNEDDS on rat hepatocytes by H2DCF assay to determine the ROS level indicated an insignificant increase in fluorescence intensity, while PTX Tween 80-SNEDDS showed nearly 20% increase in ROS levels compared to the control cells. Furthermore, histopathology examination showed the absence of any signs of inflammation from intestinal segments treated with PTX Surfactin-SNEDDS, while PTX Tween 80-SNEDDS revealed infiltration of cells and the presence of inflammation on the intestinal villous microstructures. The anticancer activity evaluation by in vitro cytotoxicity on MCF-7 cells showed PTX Surfactin-SNEDDS and PTX Tween 80-SNEDDS with IC50 of 2.65 μM and 11.52 μM, respectively, while PTX suspension showed IC50 of 18.5 μM. Moreover, blank Surfactin-SNEDDS showed IC50 of 15.23 μM, while no cytotoxicity was observed for blank Tween 80-SNEDDS. Overall, the study interpreted high suitability of biosurfactant for developing the self-nanoemulsifying formulation of PTX with enhanced bioavailability, biocompatibility and synergistic improvement in the anticancer activity over the formulations containing synthetic surfactant.