Aflatoxin B₁ (AFB₁) is a harmful and cancer-causing mycotoxin generated by Aspergillus flavus. Its mechanism of toxicity has not been fully clarified and further research is required. In this study, we attempted to further clarify aflatoxin B₁ toxicity using the results of S. cerevisiae gene expression analysis. In a Ser/Thr phosphatase 2C disruptant (ptc1Δ) with weakened activity of anti-toxic components (cell wall and membrane), the addition of low concentrations of sodium dodecyl sulfate resulted in elevated susceptibility to AFB₁. From the microarray results, expression changes in DNA synthesis or repair, sphingolipid metabolism, glucose metabolism, and cell wall-related genes were well detected. Our results indicate that AFB₁ causes sphingolipid metabolism disorder, leading to dysfunction in signal secretion and inhibition of efficient glucose metabolism, which supplies the materials for cell wall proteins and cellular components, resulting in repression of the stress response to external toxicants.