The molecules having molecular weight greater than 500 Da are considered to be ineffective in the treatment of skin diseases due to their low skin permeation. The present study entails the development of Vitamin E TPGS nanoemulsion based nanogel formulation of high molecular weight drug, Amphotericin B (AmB 923 Da), intended for effective treatment of cutaneous fungal infections. The nanoemulsion formulations were prepared in strength similar to the marketed topical formulation and optimized with respect to S mix ratio (surfactant: co-surfactant), type of surfactant, co-surfactant, globule size, size distribution, percent transmittance, dispersibility, viscosity and rheology. The optimized nanoemulsion formulation was further incorporated in gel base to form AmB nanogel formulation. As compared to marketed topical formulation, the optimized nanogel exhibited 3.9 fold higher skin deposition through porcine ear skin. Confocal laser scanning microscopy study (CLSM) showed the specific distribution of AmB in different parts of the skin and confirmed the permeation of nanogel to the deeper layers of the skin. The antifungal activity of optimized nanogel formulation tested using microdilution method was found to be 2.0 fold higher against Aspergillus niger and Candida albicans in contrast to marketed formulation. The results depicted that the prepared nanogel formulation is a better alternative for effective topical delivery of AmB.