The invention is directed to a semiconductor device having a penetrating electrode and a manufacturing method thereof in which reliability and a yield of the semiconductor device are enhanced. A semiconductor substrate is etched to form a via hole from a back surface of the semiconductor substrate to a pad electrode. This etching is performed under an etching condition such that an opening diameter of the via hole at its bottom is larger than a width of the pad electrode. Next, a second insulation film is formed on the back surface of the semiconductor substrate including in the via hole 16, exposing the pad electrode at the bottom of the via hole. Next, a penetrating electrode and a wiring layer are formed, being electrically connected with the pad electrode exposed at the bottom of the via hole 16. Furthermore, a protection layer and a conductive terminal are formed. Finally, the semiconductor substrate is cut and separated in semiconductor dies by dicing.