BACKGROUND: Cerebral ischemia-reperfusion (I/R) causes brain cell dysfunction and death. Heliox treatment shows therapeutic benefits in treating certain respiratory conditions. Here, we explore the mechanism by which heliox alleviates ferroptosis of neuronal cells injured by I/R treatment. METHOD: OGD/R-treated SH-SY5Y cells were used and screened for USPs whose expression is induced by OGD/R but suppressed by heliox treatment. Mass spectrometry was conducted to identify proteins that interact with USP46. The impact of SNX5 deficiency on the ferroptosis of USP46-overexpressing neuronal cells following sequential OGD/R and heliox treatment was also explored. Finally, the effect of USP46 overexpression on brain cell ferroptosis in a cerebral I/R rat model was explored. RESULTS: Deubiquitinase USP46 is targeted by heliox treatment in neuronal cells. USP46 expression is stimulated by I/R, and its overexpression enhances ferroptosis in I/R-treated neuronal cells. USP46 interacts with and deubiquitinates SNX5, a ferroptosis promoter, thereby increasing its stability. The knockdown of SNX5 abolishes the ferroptosis-promoting effect of USP46 in I/R-treated neuronal cells. Excessive USP46 attenuates the protective effect of heliox treatment on I/R-triggered cerebral damage in a rat model. CONCLUSION: These observations highlight the ferroptosis-promoting function of the USP46-SNX5 axis in I/R-treated neuronal cells.