Disclosed is a method of fabricating a semiconductor device. The method can include forming a gate material layer on an inner surface of a trench which extends into a part of a semiconductor substrate by passing through an insulating layer formed on the semiconductor substrate, etching the gate material layer to an initial height in the trench above a top surface of the semiconductor substrate, etching the insulating layer such that the thickness of the insulating layer is reduced, forming a gate electrode in the trench by secondarily etching the etched gate material layer, and removing the insulating layer having the reduced thickness.