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Despite the widespread agricultural use of dithianon as an antifungal agent, its neurotoxic implications for humans and wildlife have not been comprehensively explored. Using zebrafish embryonic development as our model, we found that dithianon treatment induced behavioral alterations in zebrafish larvae that appeared normal. Detailed quantitative analyses showed that dithianon at ≥0.0001 µgmL⁻¹ induced cytoplasmic and mitochondrial antioxidant responses sequentially, followed by the disruption of mitochondrial and cellular homeostasis. Additionally, dithianon at 0.01 and 0.1 µgmL⁻¹ downregulated the expressions of glutamatergic (<i>slc17a6b</i>), GABAergic (<i>gad1b</i>), and dopaminergic (<i>th</i>) neuronal markers. Contrarily, dithianon upregulated the expression of the oligodendrocyte marker (<i>olig2</i>) at concentrations of 0.001 and 0.01 µgmL⁻¹, concurrently suppressing the gene expression of the glucose transporter <i>slc2a1a</i>/<i>glut1</i>. Particularly, dithianon-induced increase in reactive oxygen species (ROS) production was reduced by both <i>N</i>-acetylcysteine (NAC) and betaine; however, only NAC prevented dithianon-induced mortality of zebrafish embryos. Moreover, NAC specifically prevented dithianon-induced alterations in glutamatergic and dopaminergic neurons while leaving GABAergic neurons unaffected, demonstrating that the major neurotransmission systems in the central nervous system differentially respond to the protective effects. Our findings contribute to a better understanding of the neurotoxic potential of dithianon and to developing preventive strategies.