According to example embodiments of inventive concepts, a method of fabricating a 3D semiconductor device may include: forming a stack structure including a plurality of horizontal layers sequentially stacked on a substrate including a cell array region and a contact region; forming a first mask pattern covering the cell array region and defining openings extending in one direction over the contact region; performing a first etching process with a first etch-depth using the first mask pattern as an etch mask on the stack structure; forming a second mask pattern covering the cell array region and exposing a part of the contact region; and performing a second etching process with a second etch-depth using the second mask pattern as an etch mask structure on the stack structure. The second etch-depth may be greater than the first etch-depth.