The fungal diseases represent an increasing global health burden and have transformed from a rare curiosity to the leading cause of human mortality. The present manuscript reports the antifungal potential of two novel compounds possessing a carbohydrate and an imidazole moiety. Antifungal susceptibility test determined the growth inhibition potential of the synthesized compounds against Aspergillus niger 9689 and it was observed that compounds D and E gave an antifungal inhibitory index of 66.66 and 56.67% respectively. Further, ultra-structure analysis of the treated fungal mycelia through scanning electron microscope (SEM) and confocal microscopy indicated significant membrane permeability and disintegration of fungal cell membrane, thus highlighting the probable role of the synthesized compounds as inhibitors of fungal lanosterol 14α-demethylase. In silico studies corroborated with the in-vitro results, as the synthesized compounds interacted with the critical amino acids present at the active site of the fungal enzyme (lanosterol 14α-demethylase).