The eye is a complex organ with a unique physiology and anatomy. Using novel nanosystems is expected to enhance ocular drug permeation and retention. Hence, this work aimed to study the potential of flexosomes as an ocular delivery system to enhance the corneal permeation and antifungal activity of Tolnaftate (TOL). Different flexosomes formulae were formulated using ethanol injection method, employing a 3.2 full factorial design. The studied formulation variables were: X: amount of stearyl amine, X: hydration volume and X: type of edge activator. Encapsulation efficiency, particle size and zeta potential were selected as dependent variables. FX5 was selected as the optimal TOL flexosomes and showed encapsulation efficiency of 66.08 ± 11.38%, particle size of 154.99 ± 29.11 nm and zeta potential of 42.95 ± 0.64 mV. FX5 was subjected to further ex vivo and in vivo studies which showed that TOL flux was significantly increased through FX5 compared to TOL suspension. Draize test and histopatholoigal tests assured that FX5 is safe to be used for eye.. The in vivo fungal susceptibility testing using Aspergillus niger demonstrated the superior and more durable antifungal activity of FX5 than TOL suspension. Hence, FX5 can be considered as promising nanocarrier for safe and efficient ocular TOL delivery.