A method for fabricating a non-volatile memory device includes repeatedly stacking interlayer dielectric layers and gate conductive layers on a substrate; etching the interlayer dielectric layers and the gate conductive layers to form cell channel holes that expose the substrate, forming a protective layer along a resultant structure, forming a capping layer on the protective layer to fill the cell channel holes, planarizing the protective layer and the capping layer until an uppermost one of the interlayer dielectric layers is exposed, forming a gate conductive layer for select transistors and an interlayer dielectric layer for select transistors on a resultant structure, etching the interlayer dielectric layer and the gate conductive layer, to form select transistor channel holes that expose the capping layer while removing the capping layer buried in the cell channel holes, and removing the protective layer.