This work aimed to analyse the damaging effects of pulsed electric fields on Rhizoctonia solani. Design Expert software was used to design an orthogonal experiment. The cell membrane damage and cell wall damage were observed by scanning electron microscopy and quantitatively determined while using a conductivity metre and an ultraviolet spectrophotometer. The results showed that the cell membrane damage rate was correlated with the voltage amplitude and processing time (p < 0.01), while the effect of pulse duration was not significant (p > 0.05). Besides, the cell wall damage was related to electric field strength (voltage amplitude) (p < 0.01), while the pulse duration and processing time had no significant effect on that (p > 0.05). The optimal process parameters for this method were 25 kV/cm, 5 min., and a pulse duration of 60 µs. The optimised conditions were tested based on these results. When compared with Control Check (CK), the cell membrane damage rate was 48.72%, which was significantly higher than CK (p < 0.01).