In a method of manufacturing a variable resistance memory device, an MTJ structure layer is formed on a substrate. The MTJ structure layer is etched in an etching chamber to form an MTJ structure. The substrate having the MTJ structure thereon is transferred to a deposition chamber through a transfer chamber. A protection layer covering a sidewall of the MTJ structure is formed in the deposition chamber. The etching chamber, the transfer chamber, and the deposition chamber are kept in a high vacuum state equal to or more than about 10−8 Torr.