In a method of manufacturing a MRAM device, a lower electrode is formed on a substrate. A first magnetic layer, a tunnel barrier layer, and a second magnetic layer are sequentially formed on the lower electrode layer. An etching mask is formed on the second magnetic layer. An ion beam etching process in which a first ion beam and a second ion beam are simultaneously emitted onto the substrate is performed to form a MTJ structure including a first magnetic layer pattern, a tunnel layer pattern, and a second magnetic layer pattern from the first magnetic layer, the tunnel barrier layer, and the second magnetic layer, respectively, the MTJ structure has no by-products remaining after the ion beam etching process is performed.