The disinfection of recirculating nutrient solution is essential to avoid disasters due to the dispersal of pathogens in closed soilless culture systems. This work presents the development of a new technique to perform disinfection, based on pulsed electric field (PEF) treatment. Hoagland solution inoculated with Fusarium oxysporum was selected as the specimen to verify the effectiveness of PEF treatment. The results indicate that PEF deactivated most Fusarium oxysporum in nutrient solution within a few seconds with the maximum disinfection efficiency achieved being 99.84%. The disinfection efficiency became higher with the extending of treatment time or the increase of PEF strength, while the initial microbial density was proven to play no role. Temperature rise indicates that PEF treatment played the dominant role in the process of disinfection. The energy efficiency depends mainly on treatment time and electric field intensity. The optimal operating conditions were found to be: treatment time less than 10 seconds and electric field strength around 5 kV/cm. This investigation implies that, in the future, PEF treatment has the potential to be applied to disinfect nutrient solution.