Chlorogenic acid (CGA) is a plant-derived compound with antifungal activity. However, the antifungal mechanism of CGA remains not fully revealed. The antifungal effect of CGA against Botrytis cinerea was assessed in the present study, and its mode of action was studied. Results demonstrated that CGA suppressed the growth of B. cinerea, as well as the development of gray mold (B. cinerea) on strawberry. Further analysis indicated that CGA induced endoplasmic reticulum (ER) stress in hyphae of B. cinerea resulting in an efflux of calcium (Ca2+) from the ER to the cytoplasm and then into mitochondria. The Ca2+ overload in mitochondria elicited the Ca2+-calmodulin-calcineurin cascade, resulting in a superoxide burst in the mitochondria. Finally, a decrease in ATP content and cell viability was observed in B. cinerea. This is the first report showing that the inhibitory effect of CGA towards B. cinerea involves an ER stress, followed by a Ca2+ release from the ER to the mitochondria, resulting in a superoxide burst and subsequent oxidative injury that reduces cell viability. Thus, CGA can be considered as an effectively substance to control gray mold on strawberry.