The antioxidant effects of natural vitamin B 6 compounds on Schizosaccharomyces pombe cells treated with menadione sodium bisulfite (water-soluble menadione and a generator of superoxide, MSB) and the mechanism underlying the function were examined with the yeast cells treated with pyridoxal 5′-phosphate. Vitamin B 6 compounds showed no ex vivo reactivity toward MBS at pH 5.5 or 7.0. The yeast cells showed no growth in the medium containing 1.0 mM MSB. The coexistence of 1.0 mM of each vitamin B 6 compound supported the growth of the yeast cells. The efficacy order was pyridoxal 5′-phosphate≥pyridoxamine 5′-phosphate>pyridoxamine>pyridoxal≥pyridoxine. The first three compounds showed higher antioxidant activity than vitamin C did. Pyridoxal 5′-phosphate prevented the reduction of the glutathione content in the MSB-treated cells and, in turn, suppressed the increases in peroxide and thiobarbituric acid reactive substances in the yeast cells and increased the viability of the yeast cells under oxidative stress. The antioxidant function of pyridoxal 5′-phosphate was not dependent on the phosphorelay pathway, which finally triggers the expression of the catalase gene.