Botrytis cinerea is a devastating postharvest pathogenic fungus causing severe postharvest decay in a wide range of fruit and vegetables. Controlling postharvest pathogens is essential to the postharvest industry. Plumbagin is a plant-derived naphthoquinone compound with various pharmacological activities, such as antioxidant, anti-inflammatory, and antimicrobial effects. However, its antifungal effects on B. cinerea have not been fully elucidated. In this study, we investigated the antifungal activity of plumbagin against postharvest fungal pathogens and elucidated its potential mechanism on B. cinerea through transcriptomics. Plumbagin exhibited broad-spectrum antifungal activity and completely inhibited the growth of various postharvest pathogens at a concentration of 20 mg L⁻¹ in vitro. Moreover, plumbagin effectively inhibited the incidence of gray mold in grape, sweet cherry, and strawberry fruit. The spore germination and viability of B. cinerea were also suppressed by plumbagin. Transcriptomic analysis indicated that plumbagin significantly affected the metabolic processes and induced autophagy in B. cinerea. Our results suggest that plumbagin is a promising broad-spectrum plant-derived fungicide that suppresses postharvest gray mold by affecting the metabolism of B. cinerea and inducing autophagy. These findings provide a theoretical basis for applying plumbagin to control postharvest pathogens.