The objective of this study was to assess the antifungal potential of plant crude extracts derived from cinnamon and rosemary against three isolates of Sclerotinia sclerotiorum under in vitro and in vivo conditions. The crude extracts were obtained using two different solvents including ethyl acetate (EA) and ethanol. The results showed that crude extracts of cinnamon are able to reduce mycelial growth of isolate 2 at volatile and contact phase by 35.4% and 78.2%, respectively. Furthermore, sclerotial myceliogenic at contact phase and carpogenic germination of isolate 2 were inhibited by 94.3% and 68.1%, respectively. In general, rosemary extracts showed less inhibitory efficacy than cinnamon. As the most effective treatment, EA extract of cinnamon was analysed using Gas Chromatography/Mass Spectrometry. The results showed the presence of 33 components and the major constituents were E-cinnamaldehyde (66.4%) followed by Alpha-Muurolene (4.86%), Alpha-Copaene (4.73%) and 2H-1-Benzopyran-2-one (3.72%). The enzyme analysis showed that the activity of phenylalanine ammonia lyase, polyphenoloxidase and peroxidase decrease in the inoculated carrots after application of plant crude extracts indicating that they cannot be considered as resistance inducers against Sclerotinia carrot rot. In conclusion, cinnamon extract was found to be more effective against the pathogen. Although crude extracts of cinnamon and rosemary were able to reduce severity of carrot rot during storage, EA extract of cinnamon (2 g L−1) was found to have practically significant effect against the disease.