Poor bioavailability of antifungal drugs due to the various protective mechanisms of the eye is a serious concern for the treatment of corneal fungal infections in today's world. The use of nanosystems that can improve the bioavailability of these antifungal drugs is relatively a new idea being conceived and here we have synthesized fluconazole loaded chitin nanogels (Flu-CNGs) which can be used for the treatment of corneal fungal infections. These nanogels were characterized using DLS, Zeta potential, SEM, FTIR and TG/DTA. The prepared Flu-CNGs have controlled release pattern which is ideal for the continuous availability of fluconazole over a longer period of time for an effective fungal treatment. Flu-CNGs are haemocompatible, cytocompatible and also showed very good cell uptake in human dermal fibroblast cells and penetration to the deeper sections of the porcine cornea with no signs of destruction or inflammation to corneal cells as shown in ex vivo permeation studies.