Purpose: To examine the association of propofol (PRO) with related key genes that may serve as potential biomarkers for alleviation of PRO-induced toxicity in neural stem cells (NSCs). Methods: Differentially expressed genes (DEGs) were screened based on GEO database, using the analysis platform of Metaboanalyst, GEO2R, DAVID and Ehbio. NSCs were purchased and treated with 3 μM of propofol (PRO). NR4A1 was transfected into NSCs, and the NR4A1 expression, apoptosis-related protein and AMPK pathway-related protein were determined by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and western blotting. Cell viability and apoptosis were evaluated by methylthiazolyldiphenyl-tetrazolium bromid (MTT) assay and flow cytometry. Results: A total of 278 DEGs were analyzed on GSE106799 microarray, and finally screened for differentially expressed down-regulated gene, NR4A1, which is a hubgene. NR4A1 expression decreased in PRO-induced NSCs. Furthermore, NR4A1 attenuated the PRO-induced decrease in the viability of NSCs and the increase in apoptosis. Moreover, NR4A1 increased p-AMPK/AMPK level. Conclusion: NR4A1 attenuates the toxicity in NSCs induced by PRO by regulating AMPK pathways, and thus provides a theoretical basis for the treatment of nerve damage caused by anesthetics.