The purpose of the present study was to develop and investigate the suitability of microemulsion based lecithin organogel formulations for topical delivery of fluconazole in order to bypass its gastrointestinal adverse effects. The ternary phase diagrams were developed and various organogel formulations were prepared using pharmaceutically acceptable surfactant (lecithin) and ethyl oleate (EO). Solubility of fluconazole in EO and EO-lecithin reverse micellar system was determined. The transdermal permeability of fluconazole from different concentrations of lecithin organogels containing EO as oil phase was analyzed using Keshary-Chien diffusion cell through excised rat skin. Solubility of fluconazole in EO-lecithin reverse micellar system was almost 3 folds higher than that in EO. Gelation and immobilization of oil require critical solubility-insolubility balance of gelator. The occurrence of gel phase was lecithin concentration dependent and was observed in 10-60% w/v of system. Organogel containing 300 mM of lecithin showed the higher drug release and better relative consistency. Hence, it was selected for antifungal activity. The increase in antifungal activity of fluconazole in lecithin organogel may be because of the surfactant action of the lecithin and EO that may help in the diffusion of drug. The histopathological data showed that EO-lecithin organogels were safe enough for the topical purpose. Hence, the present lecithin based organogel appears beneficial for topical delivery of fluconazole in terms of easy preparation, safety, stability and low cost.