A method of fabricating a semiconductor device may include forming trenches in a substrate to define a fin structure extending in a direction, forming a device isolation layer to fill the trenches, and removing an upper portion of the device isolation layer to expose an upper side surface of the fin structure. The exposing of the upper side surface of the fin structure may include repeatedly performing an etching cycle including a first step and a second step, and an etching rate of the device isolation layer to the fin structure may be higher in the second step than in the first step.