Maternal stress during pregnancy can profoundly affect offspring health, increasing the risk of psychiatric disorders, metabolic diseases, and gastrointestinal problems. In this study, the effects of high prenatal corticosterone exposure on gene expression in the brain and small intestine of rat offspring were investigated via RNA-sequencing analysis. Pregnant rats were divided into two groups: Corti.Moms were injected with corticosterone daily, while Nor.Moms were given saline injections. Their offspring were labeled as Corti.Pups and Nor.Pups, respectively. The brain tissue analysis of Corti.Pups showed that the expression levels of the genes linked to neurodegenerative conditions increased and enhanced mitochondrial biogenesis, possibly due to higher ATP demands. The genes associated with calcium signaling pathways, neuroactive ligand-receptor interactions, and IgA production were also upregulated in the small intestine of Corti.pups. Conversely, the genes related to protein digestion, absorption, and serotonergic and dopaminergic synaptic activities were downregulated. These findings revealed that gene expression patterns in both the brain and intestinal smooth muscle of offspring prenatally exposed to corticosterone were substantially altered. Thus, this study provided valuable insights into the effects of prenatal stress on neurodevelopment and gut function.