A wafer cleaning apparatus, a method of cleaning wafer and a method of fabricating a semiconductor device are provided. The method of fabricating the semiconductor device includes disposing a wafer on a rotatable chuck, irradiating a lower surface of the wafer with a laser to heat the wafer, and supplying a chemical to an upper surface of the wafer to clean the wafer, wherein the laser penetrates an optical system including an aspheric lens array, the laser penetrates a calibration window, which includes a first window structure including a first light projection window including first and second regions different from each other, a first coating layer covering the first region of the first light projection window, and a second coating layer covering the second region of the first light projection window, and the first coating layer and the second coating layer have different light transmissivities from each other.