Disclosed is a method of fabricating a light emitting diode using a laser lift-off apparatus. The method includes growing an epitaxial layer including a first conductive-type compound semiconductor layer, an active layer and a second conductive-type compound semiconductor layer on a first substrate, bonding a second substrate, having a different thermal expansion coefficient from that of the first substrate, to the epitaxial layers at a first temperature of the first substrate higher than a room temperature, and separating the first substrate from the epitaxial layer by irradiating a laser beam through the first substrate at a second temperature of the first substrate higher than the room temperature but not more than the first temperature. Thus, during a laser lift-off process, focusing of the laser beam can be easily achieved and the epitaxial layers are prevented from cracking or fracture. The laser lift-off process is performed by a laser lift-off apparatus including a heater.