Matrine is a well-known anti-inflammatory quinolizidine alkaloid derived from leguminous plant Ait. (Leguminosae). This study was designed to uncover the potential application of matrine in treating spinal cord injury (SCI). Neuron-like PC12 cells in experimental groups were pre-treated with/without matrine (200 μM) for 24 h and then stimulated by lipopolysaccharide (LPS, 5 μg/mL) for 12 h. PC12 cells in control group were cultured in complete medium. CCK-8 assay, flow cytometry, qRT-PCR, western blot and ELISA were performed to evaluate cell damage. Moreover, after cells were transfected with miR-9 inhibitor for 48 h, above indicators were tested again. qRT-PCR and western blot were also conducted to uncover the downstream effectors and signalling pathways for matrine. LPS (5 μg/mL) decreased cell viability about 50%. Matrine (200 μM) decreased cell viability about 0%, 13.8% and 30% at 24 h, 48 h and 72 h, respectively. The loss of viability, stimulation of apoptosis, and release of pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α) evoked by LPS were attenuated by the pre-treatment of matrine partly. Meanwhile, LPS reduced miR-9 expression about 60%, but matrine completely reversed LPS-decreased miR-9 level. By silencing miR-9 expression, the protective properties of matrine towards PC12 cells were impeded. Besides, matrine inhibited the activation of JNK and NF-κB pathways even under the condition of LPS. And the impact of matrine on the signalling were attenuated by miR-9 silencing. This paper provided evidence that matrine was able to protect PC12 cells against LPS-evoked damage. The neuroprotective properties of matrine may be due to its regulation of miR-9 expression as well as JNK and NF-κB pathways.