Provided is a method of manufacturing a nano-sized MTJ cell in which a contact in the MTJ cell is formed without forming a contact hole. The method of forming the MTJ cell includes forming an MTJ layer on a substrate, forming an MTJ cell region by patterning the MTJ layer, sequentially depositing an insulating layer and a mask layer on the MTJ layer, exposing an upper surface of the MTJ cell region by etching the mask layer and the insulating layer at the same etching rate, and depositing a metal layer on the insulating layer and the MTJ layer.