The fabrication of fungicides in cost-effective and eco-friendly ways is particularly important for agriculture. Plant pathogenic fungi produce many economic and ecological problems worldwide, which must be controlled with potent fungicides. Here we propose the green synthesis of fungicides, which consist of copper nanoparticles (Cu-NPs) prepared in aqueous media. Through in vitro experiments, the antifungal efficacy against Fusarium solani, Neofusicoccum sp., and Fusarium oxysporum was investigated. Although the antifungal activity differs for each fungal species, it was found that the Cu-NPs induce strong morphological changes in the mycelium. Additionally, the damage of the cell membranes of the pathogens was revealed by microscopic observations. For the three evaluated fungi, fluorescence microscopy demonstrated the intracellular generation of reactive oxygen species in the mycelium. This work proves that the green-synthesized Cu-NPs are potential fungicides against F. solani, Neofusicoccum sp., and F. oxysporum.