Glycoprotein M6A (GPM6A) is known as a transmembrane protein and an abundant cell surface protein on neurons in the central nervous system (CNS). However, the function of GPM6A in the differentiation of neurons derived from human embryonic stem (ES) cells is unknown. To investigate the function of GPM6A in neural differentiation, we generated human ES cell lines with overexpressed (B2h-oeM6A) or suppressed (B2h-shM6A) human GPM6A. Real-time polymerase chain reaction (PCR) showed that overexpression of GPM6A markedly increased the expression of neuroectodermal-associated genes (OTX1, Lmx1b, En1, Pax2, Sox2, and Wnt1), and the number of neural stem cells (NSCs) derived from B2h-oeM6A cells compared to control vector transfected human ES cells (B2h-Mock1). Our results show an increase in the number of differentiated neuronal cells (cholinergic, catecholaminergic, and GABAergic neurons) from NSCs derived from B2h-oeM6A cells. On the other hand, suppression of human GPM6A expression using a short hairpin RNA (shRNA) in human ES cells led to a decrease in both the expression of neuroectodermal-associated genes and the number of NSCs derived from B2h-shM6A cells. In addition, our results show a decrease in the number of differentiated neuronal cells from NSCs in B2h-shM6A cells compared to control vector transfected human ES cells (B2h-shNSP1). Moreover, overexpression or suppression of human GPM6A in human ES cells led to an increase or decrease, respectively, of neuronal migration. Hence, our findings suggest that expression level of GPM6A is, directly or indirectly, associated with the differentiation and neuronal migration of neurons derived from undifferentiated human ES cells.