Soy whey is a byproduct generated from the processing of several soybean products. Its valorization has continued to attract significant research interest in recent times due to the nutritional and bioactive potency of its chemical composition. Herein, the neuroprotective potency of a soy whey fermented by Cordyceps militaris SN-18 against hydrogen peroxide (H2O2)-induced oxidative injury in PC12 cells was investigated. The phenolic compositions were analyzed by high-performance liquid chromatography. Antioxidant activities were assessed by ABTS•+ scavenging assay, DPPH radical scavenging assay, reducing power assay, and ferric reducing antioxidant power assay. The neuroprotective effects of fermented soy whey (FSW) were investigated based on the oxidative injury model in PC12 cells. FSW possessed higher total phenolic content and antioxidant activities compared with unfermented soy whey (UFSW) and that most of the isoflavone glycosides were hydrolyzed into their corresponding aglycones during fermentation. The extract from FSW exhibited a greater protective effect on PC12 cells against oxidative injury by promoting cell proliferation, restoring cell morphology, inhibiting lactic dehydrogenase leakage, reducing reactive oxygen species levels, and enhancing antioxidant enzyme activities compared with that from UFSW. Additionally, cell apoptosis was significantly inhibited by FSW through down-regulation of caspase-3, caspase-9, and Bax and up-regulation of Bcl-2 and Bcl-xL. S-phase cell arrest was attenuated by FSW through increasing cyclin A, CDK1 and CDK2, and decreasing p21 protein. Fermentation with C. militaris SN-18 could significantly improve the bioactivity of soy whey by enhancing the ability of nerve cells to resist oxidative damage.