An apparatus for rubbing an alignment layer on a substrate is disclosed. The apparatus includes a platform to support the substrate; a conveyance unit incorporating the platform to convey the substrate in a predetermined direction; a rubbing roller located above the platform for rubbing the alignment layer on the substrate; a combing unit located at one side of the rubbing roller for contacting with the rubbing roller; and at least one vacuum suction unit located at one side of the platform to suck and remove the particles released from the rubbing. The combing unit serves to smoothen a rubbing cloth on the rubbing roller, with a result of low static electricity accumulation on the substrate and of a better alignment effect on the alignment layer.