Purpose The present study made an attempt to develop copper nanoparticles (Cu-NP) with antifungal property using green synthesis method. Copper oxide nanoparticles (CuO-NPs) botanically synthesized using Neem leaf extract ( Azadirachta indica A. Juss) were characterized by using different techniques like; UV–visible spectrophotometry, FTIR, XRD, SEM and TEM. Methods Materials were chosen the disease free and fresh Azadirachta indica A. Juss were collected and identified at Center of Biodiversity and Taxonomy. The plant samples were vigorously washed with distilled water then shade dried followed by sterilization with 0.1% mercuric chloride for 20 s and again it was washed with distilled water. 15 g powder form of plant material was added to 200 ml double distilled, CO 2 free and deionized water and kept in shaker at 80°C and 1500 rpm for six hours. After agitation, the extract was separated by regular centrifugation at 10,000 rpm followed by filtration by using whatmann filter paper. The final volume of 100 ml of supernatant was collected as pure extract and stored in cool place for further use. Results The final results confirm a significant inhibition of CuO-NPs for the test fungi. Additionally, CuO-NPs demonstrated an enhanced effect when combined with Neem leaf extract. A total of 20–30% improvement in activity was noticed after combination, which correlates with commonly used synthetic fungicides. The toxicity results reveal that A. indica extract and their combined fractions with CuO-NP were less toxic to the test seeds of experimental plant while as bulk Cu followed by biosynthesized CuO-NPs influenced the germination rate as compared to control pots. Conclusions The study drops a concern of research and offers a promising route of developing Copper based green fungicides that can help to combat with modern issues of synthetic fungicides. An average size of 80 ± 15 nm monoclinic cupric oxide (CuO) and cubic cuprous oxides (Cu 2 O) nanocrystals that existed in mixed form were successfully developed.