According to one embodiment, a semiconductor device includes a semiconductor substrate including a device region which is isolated by a device isolation film, a first conductive layer provided on the device region via a gate insulation film, an inter-gate insulation film provided on the first conductive layer and including an opening on the first conductive layer, a second conductive layer disposed over the device region and the device isolation film via the inter-gate insulation film, a third conductive layer provided on the first conductive layer, isolated from the second conductive layer by a peripheral trench, and connected to the first conductive layer via the opening of the inter-gate insulation film, and source/drain diffusion layers provided, spaced apart, in the device region in a manner to sandwich the first conductive layer.