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Deoxynivalenol (DON), a worldwide cereal contaminant, is mainly produced by Fusarium spp.. It not only affects the cereal quality reducing the end-use, but also poses a serious threat to food and feed safety. In order to protect human and animal health and reduce economic losses, it is important to find ways to reduce DON and mycological contamination. This study aimed to evaluate the effect of acid electrolyzed water (AcidEW) and alkaline electrolyzed water (AlkEW) with different pH values on eliminating DON and inactivating fungi in naturally contaminated wheat grains. Both AcidEW and AlkEW showed great activity on the elimination of DON and mycological contamination. The optimal pH values of AcidEW and AlkEW for DON elimination were 5.5 and 9.5, respectively. Afterwards, effects of pH 5.5 AcidEW and pH 9.5 AlkEW on F. graminearum and qualities of wheat grains were observed. AcidEW and AlkEW displayed better activity on reducing F. graminearum than pure water. Both AcidEW and AlkEW had no effect on the moisture, crude protein, wet gluten, whiteness and microstructure of wheat grains, as compared with the pure water. Moreover, AcidEW could improve farinograph property of wheat grains. Therefore, either AcidEW or AlkEW can be as a novel method to reduce DON and fungal contaminations, especially, AcidEW.