Provided is a method of manufacturing a magnetic tunnel junction that simultaneously realizes removal of oxides on side walls of a magnetic layer and formation of a protective film and prevents deterioration of magnetic characteristics. The method includes: a first step 802 of etching a stacked film including a first magnetic layer, a MgO barrier layer, and a second magnetic layer stacked in order by plasma etching using an oxidizing gas to form the magnetic tunnel junction; and a second step 803 of simultaneously introducing an organic acid gas which is an n-valent acid and a precursor gas having a corresponding metal element valence of m, to form a first protective film on side walls of the magnetic tunnel junction. In the second step, the precursor gas is introduced at a molar ratio of n/m or more with respect to 1 mole of the organic acid gas introduced.