The fluctuation of intracellular calcium concentration ([Ca2+]i) is known to be involved in various processes in the development of central nervous system, such as the proliferation of neural progenitor cells (NPCs), migration of intermediate progenitor cells (IPCs) from the ventricular zone (VZ) to the subventricular zone (SVZ), and migration of immature neurons from the SVZ to cortical plate. However, the roles of [Ca2+]i fluctuation in NPC development, especially in the differentiation of the self-renewing NPCs into neuron-generating NPCs and immature neurons have not been elucidated. Using calcium imaging of acute cortical slices and cells isolated from mouse embryonic cortex, we examined temporal changes in the pattern of [Ca2+]i fluctuations in VZ cells from E12 to E16. We observed intracellular Ca2+ levels in Pax6-positive self-renewing NPCs decreased with their neural differentiation. In E11, Pax6-positive NPCs and Tuj1-positive immature neurons exhibited characteristic [Ca2+]i fluctuations; few Pax6-positive NPCs exhibited [Ca2+]i transient, but many Tuj1-positive immature neurons did, suggesting that the change in pattern of [Ca2+]i fluctuation correlate to their differentiation. The [Ca2+]i fluctuation during NPCs development was mostly mediated by the T-type calcium channel and blockage of T-type calcium channel in neurosphere cultures increased the number of spheres and inhibited neuronal differentiation. Consistent with this finding, knockdown of Cav3.1 by RNAi in vivo maintained Pax6-positive cells as self-renewing NPCs, and simultaneously suppressing their neuronal differentiation of NPCs into Tbr1-positive immature neurons. These results reveal that [Ca2+]i fluctuation mediated by Cav3.1 is required for the neural differentiation of Pax6-positive self-renewing NPCs.