In Japan, wiping with distilled water and disinfectant ethanol is the most common method of cleaning biological safety cabinets (BSCs). In 2020, an electrolyzed water generator WOX-30WA-M2 was approved for hand disinfection. This medical device generates hypochlorite water (0.0035% hypochlorous acid and 0.015% hydrochloric acid: HClO water) and alkaline electrolyzed water (0.03% sodium hydroxide: AEW) from salt water. We investigated whether a new cleaning method for BSCs using HClO water and AEW is superior to the conventional cleaning method in removing anticancer drug residues. A model using stainless steel plates contaminated with cyclophosphamide (CPA) was prepared, and the level of CPA residue remaining after wiping was compared with the conventional method. The new cleaning method was more effective than the conventional method with respect to the level of CPA residue remaining. High-performance liquid chromatography was employed to confirm the effect of various solvents on CPA removal. The peak area of CPA decreased with increasing chlorine concentration, accompanied by the appearance of 3-chloro-CPA.Although the sum of CPA and 3-chloro-CPA areas could provide a more comprehensive evaluation of total compound recovery, accurate quantification was not feasible in this study because 3-chloro-CPA is unstable and no certified standard was available. As an alternative, we confirmed the qualitative restoration of CPA after solid-phase extraction (SPE) treatment, suggesting that the apparent loss was mainly due to reversible formation of chlorinated derivatives rather than irreversible degradation. Use of an electrolyzed water for cleaning BSCs should reduce inhalation exposure due to evaporation of residual anticancer agents and also reduce alcohol use. Sequential wipe-off of HClO water and AEW is non-corrosive to stainless steel and maintains the effectiveness of sanitization and antifouling, suggesting this is a safe method for cleaning BSCs.