Ginger is one of the cash crops grown worldwide, and consumed daily as a spice food, and utilized as Ayurvedic medicine. Soft-rot or rhizome-rot, is a major rhizome-deteriorating fungal disease caused by various fungi like Fusarium spp. and Pythium spp. in ginger, leading to huge yield losses and economic losses. This study reported in vitro antifungal activity of Phoma herbarum, cell-free extract-mediated copper oxide nanoparticles (CuONPs) against Pythium and Fusarium isolates from soft-rot infected ginger, identified at the genus level microscopically. CuONPs were detected by a visible color change from blue to dark brick red precipitate and characterized by Ultra Violet (UV)-visible spectrophotometry (absorbance maxima at 630 nm) and Nanoparticle Tracking Analysis (average size 83 nm). Stability was confirmed by Zeta potential measurement (-23.5 mV), and Face Centered Cubic crystalline structure was elucidated by X-ray diffractometry, and roughly spherical crystals were visualized by Field Emission Scanning Electron Microscopy (FESEM). Fourier Transform Infra-red (FTIR) spectroscopy showed the presence of various functional groups that stabilized CuONPs. The in vitro study showed significant antifungal activity of mycogenic CuONPs against test fungi, which was substantially comparable with a chemical fungicide, i.e., mancozeb. Accordingly, the findings supported the application of mycogenic CuONPs as a cutting-edge antifungal agent in the direction of sustainable agriculture.