A method for fabricating a physically unclonable function (PUF) device includes the steps of first defining a PUF cell region on a substrate and then performing a process to form a defect on the PUF cell region. Preferably, the formation of the defect could be accomplished by forming a shallow trench isolation (STI) on the substrate, forming a gate material layer on the substrate and the STI, patterning the gate material layer to form a first gate material layer and a second gate material layer, and then forming an epitaxial layer between and connecting the first gate material layer and the second gate material layer.