An improvement is achieved in the performance of a semiconductor device. In a method of manufacturing the semiconductor device, in an n-type semiconductor substrate, a p-type well as a p-type semiconductor region forming a part of a photodiode is formed and a gate electrode of a transfer transistor is formed. Then, after an n-type well as an n-type semiconductor region forming the other part of the photodiode is formed, a microwave is applied to the semiconductor substrate to heat the semiconductor substrate. Thereafter, a drain region of the transfer transistor is formed.