The objective of the present investigation was to develop and evaluate microemulsion based gel for the vaginal delivery of fluconazole (FLZ). The solubility of FLZ in oils and surfactants was evaluated to identify components of the microemulsion. The ternary diagram was plotted to identify the area of microemulsion existence. Various gelling agents were evaluated for their potential to gel the FLZ microemulsion without affecting its structure. The bioadhesive potential and anti-fungal activity of the FLZ microemulsion based gel (FLZ-MBG) was determined in comparison to the marketed clotrimazole gel (Candid V gel) by in vitro methods. The vaginal irritation potential of the FLZ-MBG was evaluated in rabbits. The clinical efficacy of the FLZ-MBG and Candid V gel was evaluated in females suffering from vaginal candidiasis. The FLZ microemulsion exhibited globule size of 24 nm and polydispersity index of 0.98. Carbopol ETD 2020 could successfully gel the FLZ microemulsion without disturbing the structure. The FLZ-MBG showed significantly higher (P<0.05) in vitro bioadhesion and anti-fungal activity as compared to that of Candid V gel. The FLZ-MBG did not show any signs of vaginal irritation in the rabbits. The small-scale clinical studies indicated that the FLZ-MBG shows faster onset of action than Candid V gel although no difference was observed in the clinical efficacy.