Disclosed are an apparatus and method for fabricating an alignment layer for liquid crystal displays, capable of shortening process time, preventing scratches of alignment layers and decreasing black luminance. The method includes coating an alignment agent on a substrate, arranging a nano pattern mold with a groove and a protrusion to contact the alignment agent, pre-curing the alignment agent, separating the nano pattern mold from the alignment agent, and hard-curing the alignment agent separated from the nano pattern mold to form an alignment layer.