Dioscorea nipponica, a perennial herb growing in mountainous areas, has been used as a folk medicine for asthma, rheumatoid arthritis, bronchitis, and other disease in Korea, whereas the effect of this plant on cancer cells has not been clearly clarified. Cellular cytotoxicity was examined by cell viability assay and DNA fragmentation by DNA ladder assay. Activation of different protein expression was detected by western blot analyses. We first demonstrated that D. nipponica extract (DNE) reducing the SH-SY5Y cell viability with $IC_{50}$ of $27.57{mu}g/mL$ at 24 h. However, DNE downregulated the expression of antiapoptotic protein includes B-cell lymphoma-2 (Bcl-2), B-cell lymphoma-extra large (Bcl-xL), and myeloid cell leukemia 1 (Mcl-1) which also activated cleaved caspase-9 and caspase-3 in a dose- and time-dependent manner. Consequently, DNE-induced cytotoxicity was not mediated by the Fas/FasL, phosphatidylinositide-3 kinase/AKT/glycogen synthase kinase-$3{eta}$ (PI3K/AKT/GSK-$3{eta}$), and mitogen activated protein (MAP) kinases signaling pathway. In addition, DNE-induced cells shown damage morphology which had become cell rounding, neurite retraction, membrane blebbing, is right spell blebbing, and shrunken in a dose- and time-dependent manner that clearly indicate this morphological change might be due to the process of apoptosis which shown fragmented DNA. These results indicate that apoptotic effects of DNE on SH-SY5Y cells are mediated by intrinsic mitochondrial caspases signaling pathway, suggesting that DNE might be effective as an anticancer agent for neuroblastoma malignancies.