Postharvest diseases severely deteriorate the intrinsic quality and commercial value of fruits and vegetables, leading to significant economic losses for farmers and increased costs for consumers. In the present study, rapamycin was effective in suppressing mycelial growth of Botrytis cinerea and disease severity of gray mold on harvested apple, pear and grape fruits. The inhibitory mechanism was attributed to a modulation in autophagic activity and membrane permeability rather than the induction of reactive oxygen species. Increases in the degree of membrane peroxidation and the leakage of cytosolic contents were also detected, supporting the data on reduced cell viability. The results indicated that rapamycin may be a promising alternative for controlling gray mold caused by B. cinerea on harvested produce.