A method of fabricating an MTJ device is provided including the following process. A first via is formed in the first dielectric layer. A first electrode layer is formed on the first dielectric layer and the first via. An MTJ stack layer is formed on the first electrode layer. A patterned second electrode layer is formed on the MTJ stack layer and used as a mask. A first ion beam etching process is performed to etch the patterned second electrode layer and pattern the MTJ stack layer and the first electrode layer to form a second electrode, an MTJ stack structure, and a first electrode. A first protective layer is formed to cover the second electrode and the MTJ stack structure. A second ion beam etching process is performed to remove a portion of the MTJ stack structure and a portion of the first electrode.