Abstract Aim We tested the hypothesis that low testosterone alters the effects of intermittent hypoxia (IH) on glucose homeostasis, hepatic oxidative stress, and transcriptomic profile in male mice. Methods We used sham‐operated or orchiectomized (ORX) mice exposed to normoxia (Nx) or IH for 2 weeks. We performed fasting insulin and glucose tolerance tests and assessed fasting and postprandial insulin resistance with the HOMA‐IR. The activity of hepatic prooxidant (NADPH oxidase—NOX), antioxidant enzymes (superoxide dismutase, catalase, and glutathione peroxidase—SOD, Cat, GPx), lipid peroxidation (MDA concentration), and the total concentration of glutathione (GSH) were measured under postprandial conditions. mRNA sequencing and pathway enrichment analyses were used to identify hepatic genes underlying the interactions between IH and testosterone. Results In Sham mice, IH improves fasting insulin sensitivity and glucose tolerance, while there are no effects of IH in ORX mice. In ORX mice, IH induces postprandial hyperinsulinemia, insulin resistance, and a prooxidant profile of enzyme activity (low SOD activity) without altering hepatic MDA and GSH content. ORX and IH altered the expression of genes involved in oxidoreductase activities, cytochromes‐dependent pathways, and glutathione metabolism. Among the genes upregulated in ORX‐IH mice, the flavin‐containing monooxygenases (FMO) are particularly relevant since these are potent hepatic antioxidants that could help prevent overt oxidative stress in ORX‐IH mice. Conclusion Low levels of testosterone in male mice exposed to IH induce post‐prandial hyperinsulinemia and insulin resistance and determine the mechanisms by which the liver handles IH‐induced oxidative stress.