Provided is a semiconductor device including a substrate having a first conductivity type, an isolation structure, a well region having the first conductivity type, a gate structure, and doped regions having a second conductivity type. The isolation structure is disposed in the substrate to form an active region of the substrate. The well region is disposed in the active region and surrounds sidewalls of the isolation structure to form a native region in the active region. The gate structure is disposed over the substrate in the native region. The doped regions are disposed respectively in the well region and the native region of the substrate at two sides of the gate structure. A method of fabricating the semiconductor device is also provided.