The purpose of this study was to optimize the extraction process of polysaccharides from the stems of Panax ginseng C. A. Meyer using different solvents (water, acid and alkali), and investigate their protective effects on PC12 cells against Amyloid-β1–42 (Aβ1–42)-induced cell apoptosis. Three polysaccharides (W-GSP, Ac-GSP and Al-GSP) were prepared and optimized: liquid to material ratio 27:1 mL/g, extraction temperature 89°C, extraction time 2.9 h and 0.3 mol/L HCl/NaOH. The results of characterization indicated that the monosaccharides of W-GSP (703.80 kDa), Ac-GSP (641.38 kDa) and Al-GSP (457.04 kDa) all composed mannose, rhamnose, glucuronic acid, galacturonic acid, glucose, galactose, xylose and arabinose with different molar ratios. Interestingly, W-GSP possessed a lower uronic acid, higher molecular weight, rougher surface and poorer thermal stability, whereby W-GSP exhibited a protective effect against Aβ1–42-induced apoptosis in PC12 cells by mediating the JNK signaling pathway, restoring the mitochondrial membrane potential and reducing intracellular ROS levels. This study should be provided the theoretical basis for the study and exploitation of polysaccharides from the stems of Panax ginseng C. A. Meyer.