In a method of manufacturing a semiconductor device including a magnetic random access memory (MRAM) cell, a first layer made of a conductive material is formed over a substrate. A second layer for a magnetic tunnel junction (MTJ) stack is formed over the first conductive layer. A third layer is formed over the second layer. A first hard mask pattern is formed by patterning the third layer. The MTJ stack is formed by patterning the second layer by an etching operation using the first hard mask pattern as an etching mask. The etching operation stops at the first layer. A sidewall insulating layer is formed over the MTJ stack. After the sidewall insulating layer is formed, a bottom electrode is formed by patterning the first layer to form the MRAM cell including the bottom electrode, the MTj stack and the first hard mask pattern as an upper electrode.