Boron-doped diamond anodes and stainless-steel cathodes were employed in an electrochemical flow cell and evaluated for inactivation efficacy on the plant pathogen Rhizoctonia solani J.G. Kühn [Thanatephorus cucumeris (A.B. Frank) Donk] in hydroponic fertigation water. The electrochemical system showed promise as an electrochemical advanced oxidation process (EAOP) in that significant reductions in R. solani (AG-8) were achieved; however, to achieve complete inactivation the system required supplemental chloride (20 mg L^-1), while using 9.09 mA cm^-2. The chloride allowed for low levels of free chlorine (≤0.17 mg L^-1) that were more active in the bulk solution, complementing the electrode surface EAOP reactions. Perchlorate production was an initial concern but was found to be negligible under the conditions tested. Small but significant increases in nitrate, ammonium, and sulphate were observed following treatment. These increases are hypothesized to originate from the degradation of proteins and amino acids released during pathogen cell disruption.