A semiconductor device includes an element isolation insulating film adjacent to an active area, a gate insulating film formed on a semiconductor substrate in the active area, paired gate electrodes located on the gate insulating film, a contact plug located on the active area between the gate electrodes, a pair of first upper lines located on the gate electrodes, a second upper line located on the gate electrodes, and a stopper film above upper surfaces of the gate electrodes and side surfaces of the gate electrodes. The element isolation insulating film has a first height of an upper surface thereof with reference to an upper surface of the semiconductor substrate and a second height of another upper surface thereof with reference to another upper surface of the semiconductor substrate. The first height is smaller than the second height.