Deoxynivalenol (DON) is a common mycotoxin, which is known to be extremely harmful to human and livestock health. In this study, DON was degraded by electrochemical oxidation (ECO) using a graphite electrode and NaCl as the supporting electrolyte. The graphite electrode is advantageous due to its electrocatalytic activity, reusability, and security. The degradation process can be expressed by first-order kinetics. Approximately 86.4% of DON can be degraded within 30 min at a potential of 0.5 V. The degradation rate reached 93.2% within 30 min, when 0.5 V potential was used for electrocatalyzing a 10 mg/L DON solution. The degradation rate of DON in contaminated wet distiller’s grain with solubles (WDGS) was 86.37% in 60 min. Moreover, results from the cell counting kit-8 (CCK-8) and 4,6-diamidino-2-phenylindole dihydrochloride (DAPI) staining assay indicated that ECO reduced the DON-induced cytotoxicity and apoptotic bodies in a gastric epithelial cell line (GES-1) compared to the DON-treated group. These findings provide new insights into the application of ECO techniques for degrading mycotoxins, preventing food contamination, and assessing DON-related hazards.