Neuroblastoma is the most common solid tumor in children. Current therapy modalities have resulted in little amelioration in the cure rate of neuroblsatoma and therefore, outlining biologically based therapies for neuroblastoma remains of main priority. This study was carried out to appraise the impeding effects of silibinin, a potent anti-cancer agent, on two different neuroblastoma cell lines, stromal SK-N-MC and neuroblastic SK-N-BE(2) cells. The microculture tetrazolium assay, gelatin zymography, colony formation assay, cell cycle distribution survey, apoptosis assay, and quantitative real-time reverse transcription-PCR were applied to evaluate the effects of silibinin on metabolic activity, gelatinolytic activity of MMP-2 and MMP-9, surviving potential, cell cycle, apoptosis, and expression pattern of the genes involved in cell survival and invasion of the two neuroblastoma cell lines. Treatment for 48 h inhibited metabolic activity and clonogenic potential of SK-N-MC cells in a dose-dependent manner. Silibinin also inhibited transcriptional levels of MMP-2, MMP-9, and uPAR, as markers of cell invasion, in SK-N-MC cells. Higher concentration of silibinin (75, 100 μM) suppressed enzymatic activity of MMP-2 in this cell line. No change in apoptosis and cell cycle was observed in neither of the cells after treatment with silibinin. On the other hand, silibinin highly decreased mRNA expression of Akt, and NF-κB1 and its regulators, IKK1 and IKK2 in SK-N-MC cell line. Comparison of transcriptional expression of Akt, and NF-κB1 in untreated stromal and neuroblastic cell lines shows that their basal transcriptional levels are much higher in SK-N-BE(2) cell line than that in SK-N-MC cells. It seems that SK-N-BE(2) cell line probably resists to silibinin through higher expression of Akt and probably NF-κB1. Collectively, our results demonstrated that silibinin highly inhibits the proliferative potentials of SK-N-MC cell line, whilst it had less inhibitory effect on SK-N-BE(2) cell line. Our results suggest that suppression of SK-N-MC cell line by silibinin may be through inhibition of Akt-mediated NF-κB1.