A manufacturing method of a semiconductor device includes: (a) forming a gate structure for a control gate electrode on a semiconductor substrate; (b) forming a charge storage film so as to cover a first side surface, a second side surface, and an upper surface of the gate structure; (c) forming a conductive film for a memory gate electrode on the charge storage film; (d) removing a part of the charge storage film and a part of the conductive film such that the charge storage film and the conductive film remain in this order on the first side surface and the second side surface of the gate structure, thereby forming the memory gate electrode; and (e) removing apart of the gate structure separate from the first side surface and the second side surface such that a part of the semiconductor substrate is exposed from the gate structure.