Background: Nitric oxide (NO) is a reactive free radical gas and a messenger molecule. NO has many physiological functions, but excessive NO production induces neurotoxicity. Objective: The present study investigated whether the aqueous extract of Polygala tenuifolia Willdenow possesses a protective effect on NO-induced apoptosis in human neuroblastoma cell line SK-N-MC. Method: For this study, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, 4,6-diamidino-2-phenylindole (DAPI) staining, terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick end labeling (TUNEL) assay, DNA fragmentation assay, reverse transcription-polymerase chain reaction (RT-PCR), Western blot, and caspase-3 enzyme assay were performed. Result: Sodium nitroprusside (SNP) exposure significantly decreased the viability of cells. The cells treated with SNP exhibited several apoptotic features such as increasing of Bax expression, caspase-3 enzyme activity and inhibiting of Bcl-2 expression. On the other hand, the viability of cells pre-treated with the aqueous extract of Polygala tenuifolia Willdenow was increased dose-dependently. The cells pre-treated for 1 h with the aqueous extract of Polygala tenuifolia Willdenow followed by treatment with SNP showed a decreased occurrence of apoptotic features like decreasing Bax expressions, caspase-3 enzyme activity and increasing Bcl-2 expressions. The aqueous extract of Polygala tenuifolia Willdenow reduced apoptotic cell death in neuroblastoma cell line SK-N-MC through the inhibition of Bax-dependent caspase-3 activation and the increasing of Bcl-2 expression. Conclusion: Based on the present results, it is possible that Polygala tenuifolia Willdenow has therapeutic value for the treatment of a variety of NO-induced brain diseases.