A method of manufacturing a field effect transistor can prevent increase of a sheet resistance of a metal silicide layer formed on a gate electrode. In this method of manufacturing the field effect transistor, gate electrode protective layers are formed on the gate electrodes. Using the gate electrode layers as a mask, impurity is ion-implanted into a semiconductor substrate to form source/drain regions. Thereby, the ion implantation for forming the source/drain regions can be performed without ion-implanting the impurity into top surfaces of the gate electrodes. As a result, increase of a sheet resistance of the metal silicide layer, which is formed on the top surfaces of the gate electrodes, is prevented. The use of rotary implantation and of gate protective layer including a silicon oxide film and an etching stopper layer formed on the oxide film is also disclosed.