Programming a variable resistance element includes: a writing step of applying a writing voltage pulse to transition metal oxide comprising two stacked metal oxide layers to decrease resistance of the metal oxide, each metal oxide layer having different oxygen deficiency; and an erasing step of applying an erasing voltage pulse, of different polarity than the writing pulse, to the metal oxide to increase resistance of the metal oxide. |Vw1|>|Vw2|, Vw1 representing voltage of the writing pulse for first to N-th writing steps, and Vw2 representing voltage of the writing pulse for (N+1)-th and subsequent writing steps, N being at least equal to 1, te1>te2, te1 representing pulse width of the erasing pulse for first to M-th erasing steps, and te2 representing pulse width of the erasing pulse for (M+1)-th and subsequent erasing steps. M>1. The (N+1)-th writing step follows the M-th erasing step.