Provided is a method of manufacturing a semiconductor device. After a semiconductor wafer is placed over a wafer stage with which a dry cleaning chamber of a film forming apparatus is equipped, dry cleaning treatment is given over the surface of the semiconductor wafer with a reducing gas. Then, the semiconductor wafer is heat treated at a first temperature of from 100 to 150° C. by using a shower head kept at 180° C. The semiconductor wafer is then vacuum-transferred to a heat treatment chamber, wherein the semiconductor wafer is heat treated at a second temperature of from 150 to 400° C. A product remaining over the main surface of the semiconductor wafer is thus removed. The present invention makes it possible to manufacture a semiconductor device having improved reliability and production yield by reducing variations in the electrical properties of a nickel silicide layer.