A method of manufacturing an MRAM device includes sequentially forming a first insulating interlayer and an etch-stop layer on a substrate. A lower electrode is formed through the etch-stop layer and the first insulating interlayer. An MTJ structure layer and an upper electrode are sequentially formed on the lower electrode and the etch-stop layer. The MTJ structure layer is patterned by a physical etching process using the upper electrode as an etching mask to form an MTJ structure at least partially contacting the lower electrode. The first insulating interlayer is protected by the etch-stop layer so not to be etched by the physical etching process.