The fungicide prochloraz was subjected to degradation by the pathogen causing rice Bakanae disease, Fusarium fujikuroi, in order to gain an insight into the mechanisms of sensitivity and resistance to the fungicide. Growth-inhibiting assays of pathogens conducted on potato dextrose agar (PDA) plates by a paper-disc agar-diffusion method. Significant growth inhibition of the sensitive strain CF106 was observed at the recommended treatment level of prochloraz, whereas negligible growth inhibition of the resistant strain CF245 was observed at the same treatment level. The strain CF245 was shown to be able to grow on PDA with 500 mg/L of the fungicide, which is significantly higher than its recommended treatment level. Growth-inhibiting assays of pathogens were also conducted in potato dextrose broth (PDB) medium supplemented with prochloraz at different concentrations, measuring their biomass weights over the incubation period. Significant growth inhibition was observed in the strain CF106 at a level of 0.5 mg/L, but negligible growth inhibition was observed in the strain CF245 at the same treatment level with the strain CF106. The strain CF245 could grow in PDB supplemented with 1.0 mg/L of prochloraz. The degradation of prochloraz by the two strains was evaluated by gas liquid chromatography and mass spectrometry analyses. The strain CF245 completely degraded 1.0 mg/L of prochloraz in 5 days after incubation, whereas no degradation of prochloraz was observed by the strain CF106 at the same treatment level. Liquid chromatography Q-TOF MS detected N-(2-(2,4,6-trichlorophenoxy)ethyl)propan-1-amine as a major degradation product of prochloraz by the strain CF245. These results indicated that the degradation of prochloraz may account for the reduced sensitivity of the strain CF245 to prochloraz.