The effects of electrolyzed water on the elimination of aflatoxin B1 (AFB1), aflatoxin B2 (AFB2), aflatoxin G1 (AFG1), aflatoxin G2 (AFG2) and ochratoxin A (OTA) standard solutions (50 μg/L) were explored in the present study. Acidic electrolyzed water solutions (AcEW-1, AcEW-2 and AcEW-3) and alkaline electrolyzed water solutions (AlEW-1, AlEW-2 and AlEW-3) were prepared via the electrolysis of sodium chloride solutions at concentrations of 1.5, 2.0, and 2.5 g/L, respectively, and their abilities to eliminate five mycotoxins from artificially contaminated semi-dried fish products (2 ± 0.5 g, 40 μg/kg) were compared. Additionally, this ability was also compared among AcEW-3, AlEW-3, and de-ionized water(DW). The results showed that alkaline electrolyzed water could effectively eliminate five mycotoxin standards with elimination rates of more than 90%. The elimination effect of AcEW-3 on the five mycotoxins was better than that of AcEW-1 and AcEW-2. There were no significant differences in the elimination effects of AlEW-1, AlEW-2, and AlEW-3 on the five mycotoxins (p > 0.05). The elimination effects of AcEW-3 and AlEW-3 on aflatoxin were significantly higher than that of DW (p < 0.05), but no significant differences were found (p > 0.05) between AcEW-3 and AlEW-3. The elimination effect of AlEW-3 on OTA was significantly higher than that of AcEW-3 and DW (p < 0.05). Therefore, alkaline electrolyzed water can be used to soak semi-dried fish products to remove the residual salts, eliminate potential mycotoxins, and reduce the occurrence of food safety issues caused by mycotoxins.