The aim of the present study was to isolate fungal pathogens from various type of sorghum seeds collected from different districts. A total of 98 seeds were procured from 14 regions. The surface sterilization of seeds with 2% sodium hypochlorite was done by following Parsa, 2016 methods, and then sterilized seeds were placed on potato dextrose agar plates having streptomycin (50μg/ml) as an antibacterial drug by using Otero et al., 2002 method. The identification of isolated fungi was occurred via morphological studies. The identified fungal isolates include Alternaria alternate, Curvularia lunata, and Fusarium moniliforme that produce many economic and ecological problems worldwide. Integration of nano-science in medicine leads to the development of biomedical products that help society in a faster and safer manner. Here, copper nanoparticles were synthesized by using methanol leaf extracts of Azadirachta indica (AIL) and Moringa oleifera (MOL) and their characterization was done through UV-visible spectroscopy and SEM. The synthesized CuNPs-AIL and CuNPs-MOL were irregular in shape with an average size of 100 nm and 80 nm, respectively. CuNPs-MOL showed highest antifungal activity with 1548.02 and 690.8 inhibition annulus (IA) against Curvularia lunata, and Fusarium moniliforme as compared to the CuNPs-AIL. Furthermore, both synthesized nanoparticles exhibited same IA value against Alternaria alternate. Overall, CuNPs-AIL and CuNPs-MOL were more effective as antifungal agents. The results suggest that fungal infection in sorghum seeds can be controlled using eco-friendly and cost effective plant-based synthesized CuNPs. This work engages further identification of fungal pathogens based on 18S rRNA sequencing and in vivo treatment with plant-based copper nanoparticles to inhibit the growth of isolated fungal strains on sorghum seed.